title: FT H3ac (non-exposed)

status: Public on Feb 28 2018

type: genomic

city: changsha

first: Shu

last: Ding

state: hunan

address: Tongzipo street 138#

country: China

institute: The Third Xiangya Hospital

description: Chip-chip FT epidermal sheet H3ac

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4μg of Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Processed data files include scaled, log2 (ChIP/Input) ratio.

molecule: genomic DNA

organism: Homo sapiens

source_name: H3ac ChIP DNA from non-exposed Pool

label_protocol: The Immunoaffinity-enriched DNA was amplified using a WGA kit from Sigma-Aldrich (GenomePlex® Complete Whole Genome Amplification (WGA2) kit). The amplified DNA samples were then purified with QIAquick PCR purification kit (Qiagen). The purified DNA was quantified using a nanodrop ND-1000. For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen ChIP-on-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Epidermis samples were pulverized and chemically crosslinked by 1% formaldehyde. Cells were rinsed twice with PBS and lysed using lysis buffer (0.1% SDS, 0.5% Triton X-100, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl, protease inhibitor, Roche). Lysed cells were sonicated using a Diagenode Bioruptor UCD-200 at high power in ice water. Sonicated fragments ranged in size from 200 to 1000 bp. After sonication, samples were centrifuged at 13,000 ×g for 10 min. The supernatant was pre-absorbed by 50 μl protein A/G beads (Santa Cruz) and incubated with magnetic beads conjugated antibodies (H3 Acetylation Antibody) overnight at 4 °C. The beads were then washed four times by lysis buffer, two times by LiCl buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]), and three times by TE buffer. The bound immunocomplex was eluted by adding 300 μl fresh elution buffer (1% SDS, 0.1 M NaHCO3). Twenty microliters of 5M NaCl was then added to the eluted product and incubated at 65 °C overnight to reverse the crosslinking. Immunoprecipitated genomic DNA was then puriﬁed using a QIAGEN Puriﬁcation Kit and dissolved in EB buffer for the following qPCR QC assay or ChIP-chip analysis.

treatment_protocol: The epidermis and the dermis are separated by incubating the skin fragments overnight at 4 °C in 0.2% dispase solution, then peeling epidermal sheet with forceps.

tag: gender

value: Female

tag: tissue

value: Skin

tag: region

value: Buttock

tag: chip antibody

source_name: Input DNA from non-exposed Pool

value: none, input DNA


title: FS H3ac (sun-exposed)

description: Chip-chip FS epidermal sheet H3ac

source_name: H3ac ChIP DNA from sun-exposed Pool

value: Outer forearm

source_name: Input DNA from sun-exposed Pool


title: 24h

type: SRA

city: Zhenjiang

first: Pingzhen

last: Xu

state: Jiangsu

address: sibaidu road 16

department: School of Biotechnology,

institute: Jiangsu University of Science and Technology

description: Dazao silkworm

library_source: transcriptomic

data_processing:
Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2000 system
Clean reads were screened by filtering out low-quality reads
A second quality analysis for alignment, analysis of the distribution and coverage of the clean reads on the reference sequence was conducted
The sequences were aligned to the silkworm genome database SilkDB.
PKM (Per Kb per Million reads) was used to calculate the expression level of genes, with PKM=mapped reads of gene/(the total mapped reads of all genes*the length of this gene)*10^9. TheRPKM of a gene ranged up to 5, and difference in expression was considered at P < 0.05.The genes with FDR≤0.01 and |log2 Ratio|≥1 are defined as the DEGs. Gene expressions were compared following two strategies: (Ⅰ) Samples of four time points except 0h compared with the sample of 0h. (Ⅱ) Each sample was compared with the sample of the prior point in time.
Genome_build: SilkDB (http://silkworm.swu.edu.cn/silkdb/)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The processed data include the PKM of the five samples.a gene and its log2 Ratio of TPM among all time points would be selected if it is a DEG in any comparison. The expression patterns were clustered using hierarchical cluster analysis. The Pearson's correlation of log2 Ratio among the genes is being used as the distance for clustering.

molecule: total RNA

organism: Bombyx mori

source_name: eggs

growth_protocol: The silkworm strain Dazao was provided by The Sericulture Research Institute, Chinese Academy of Agricultural Sciences (Zhenjiang, China). Then they were reared under standard conditions until spawning (25˚C and 70% humidity). Unfertilized embryos were collected at specific times (0h, 6h, 12h, 18h, 24h). 0h is defined as the 15th minute after most female moths spawning. The condition during the embryos collection is 25˚C and 70% humidity with 12h light/12h dark photoperiod. All samples were immediately stored in liquid nitrogen.

extract_protocol:
Total RNA was extracted from embryos at various times using total RNA isolation kit (Qiagen, USA) in accordance with the manufacturer’s instructions. The mRNA was purified by Oligo(dT) magnetic beads (Invitrogen, USA), then used as templates for cDNA synthesis.
The 5' ends of tags were generated by endonuclease NlaⅢ, which recognizes and cut off the CATG sites on cDNAs. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. The raw tags were sequenced by Illumina HiSeqTM 2000. Clean tags were generated by removing 3' adaptor sequence, low quality tags, tags with a copy number of 1 and tags which were too long or too short, leaving only the tags of 21 bp long.

value: female

tag: sample type

value: unfertilized eggs


title: Control.2

type: RNA

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: The data were analyzed using R and R packages as follows: the normalization by Robust Multi-array Average (RMA) via the oligo package and the application of moderated t-statitsics via the limma package.

label: biotin

organism: Mus musculus

source_name: Muscle from Control mouse #2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instruction (Invitrogen).

value: Gastronemious muscle

tag: genotype

value: Floxed TAK1


title: 12h

description: Dazao silkworm


title: RWP-1_Ctrl_2_1

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

hyb_protocol: Samples was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples in the statistical environment R

label_protocol: 100ng of total RNA from each sample was processed and labelled according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2) (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted following Quiagen protocol

tag: cell line

tag: cell type

value: pancreatic cancer cell line

tag: treated with

value: none (Ctrl)


title: 18h

description: Dazao silkworm


title: KO.1

source_name: Muscle from TAK1 KO mouse #1

value: muscle-specific TAK1-knockout


title: RWP-1_rGAL1_2_2


title: 6h

description: Dazao silkworm


title: KO.3

source_name: Muscle from TAK1 KO mouse #3


title: Control.1

source_name: Muscle from Control mouse #1


title: Control.3

source_name: Muscle from Control mouse #3


title: KO.2

source_name: Muscle from TAK1 KO mouse #2


title: 0h

description: Dazao silkworm


title: RWP-1_rGAL1_1_2


title: RWP-1_Ctrl_1_1


title: HCT MS

city: Mainz

first: Oliver

middle: H.

last: Krämer

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

country: Germany

institute: University Medical Center

hyb_protocol: Hybridization for 16 hours at 45°C in Affymetrix Hyb oven Genechip 640. Genechips were washed and stained according to protocol on Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on Affymetrix Genechip Scanner 3000 7G.

data_processing: .CEL files which are given are raw data files. CEL files were generated automatically by Affymetrix Command Console software acording default settings. For further data processing, Robust Multichip Analysis (RMA) Algorithm was used.

label: Biotin

source_name: HCT116 cells_treated with 2 µM MS-275 for 24 h

label_protocol: Labelling with biotin was performed using the Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays starting with 100 ng total RNA.

growth_protocol: HCT116 cells were cultured in Dulbecco´s modified Eagle´s medium (GE Healthcare) supplemented with 10% fetal calf serum (Sigma-Aldrich) and 50 µg/ml Gentamicin (GE Healthcare).

extract_protocol: Total cellular RNA was isolated by Trizol extraction with peqGOLD RNAPureTM according to the manufacturer´s protocol.

treatment_protocol: 24 h after seeding, HCT116 cells were treated with 1 mM hydroxyurea (HU) and/or 2 µM MS-275 (MS) for 24 h. Cells were harvested using accutase (GE Healthcare).

value: colorectal cancer cell line


title: HCT HU+MS

source_name: HCT116 cells_treated with 1 mM HU and 2 µM MS-275 for 24 h


title: HCT HU

source_name: HCT116 cells_treated with 1 mM HU for 24 h


title: HCT Ctrl

source_name: HCT116 cells_untreated


title: CCAT2-G overexpressing bone marrow, biological rep3

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: 5 µg of total RNA was reverse transcribed with an oligo(dT) primer that has a T7 RNA polymerase promoter at the 5’ end. Second-strand synthesis was followed by cRNA production with incorporation of biotinylated ribonucleotides using the BioArray High Yield RNA Transcript Labeling Kit T3 from Enzo Life Sciences (Farmingdale, NY). The labeled cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 230 4.0 arrays.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: GeneSpring GX software v.13 (Agilent Technologies) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

source_name: Mus musculus CCAT2-G overexpressing bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow cells were extracted from mice under sterile conditions. Cells were flash frozen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C57Bl6 mice were genetically engineered to overexpress CCAT2-G or CCAT2-T in all tissues of the body.

tag: strain

value: Bone marrow

value: CCAT2-G overexpressing

tag: drai status

value: DRAI-


title: WT DC control (immature DC)

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

description: cultured primary cells

hyb_protocol: cRNA was hybridized to the GeneChip Mouse MOE 430 2.0 (Affymetrix) according to the manufacturer instructions.

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high-resolution scanner.

data_processing: Expression values were obtained after analysis of data with MAS5.0 algorithm

source_name: cultured mouse dendritic cell

label_protocol: Biotinylated cRNA was generated using two cycle target preparation kit (Affymetrix) following manufacturer's instructions and performed at the Servicio de Genomica, Universidad Complutense de Madrid

growth_protocol: BM-derived DCs (BMDCs) from LXR WT and LXR double knockout (combined deficiency of LXRalpha and LXRbeta) mice were generated in vitro as described by Inaba et al. (J Exp Med. 1992 Dec 1;176(6):1693-702) with modifications. BM cells were cultured for 6-7 days in RPMI 1640 medium containing 10% fetal bovine serum (FBS) supplemented with mouse GM-CSF (20 ng/mL, Peprotech, UK) every two days. Non-adherent cells were collected and further enriched in CD11c positive DCs by positive selection with CD11c microbeads (MiltenyiBiotec) following the manufacturer instructions.

extract_protocol: After treatment, RNA was harvest by column purification with RNAeasy mini-kit (Qiagen). RNA was quantified and submitted for microarray analysis to the Unidad de Genomica, Universidad Complutense de Madrid (UCM)

treatment_protocol: Bone Marrow-derived Dendritic cells were cultured with GMCSF (10ng/ml) as control cells or GMCSF + LPS (100ng/ml) for 24 hours as a stimulus for DC maturation.

value: bone marrow-derived dendritic cell (GM-CSF)

tag: culture condition

value: GMCSF

tag: genotype/variation

value: WT


title: CCAT2-GT overexpressing bone marrow, biological rep5

source_name: Mus musculus CCAT2-GT overexpressing bone marrow

value: CCAT2-GT overexpressing

value: DRAI+


title: LXR-DKO +LPS 24h (mature DC)

description: cultured primary cells

value: GMCSF + LPS

value: LXR-DKO


title: CCAT2-GT overexpressing bone marrow, biological rep6


title: CCAT2-GT overexpressing bone marrow, biological rep2


title: WT bone marrow, biological rep4

source_name: Mus musculus WT bone marrow


title: tumor1

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg19
Supplementary_files_format_and_content: xls files include RPKM values for each Sample

source_name: Derived from 1st RB patient

extract_protocol:
Retinoblastoma and peri-tumor samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retinoblastoma tumor

tag: diagnosis

value: Retinoblastoma


title: tumor2

source_name: Derived from 2nd RB patient


title: CCAT2-T overexpressing bone marrow, biological rep2

source_name: Mus musculus CCAT2-T overexpressing bone marrow

value: CCAT2-T overexpressing


title: CCAT2-G overexpressing bone marrow, biological rep4


title: CCAT2-GT overexpressing bone marrow, biological rep1


title: CCAT2-T overexpressing bone marrow, biological rep1


title: CCAT2-G overexpressing bone marrow, biological rep2


title: LXR-DKO DC control (immature DC)

description: cultured primary cells


title: tumor3

source_name: Derived from 3rd RB patient


title: WT bone marrow, biological rep1


title: WT bone marrow, biological rep2


title: CCAT2-T overexpressing bone marrow, biological rep4


title: CCAT2-G overexpressing bone marrow, biological rep1


title: CCAT2-T overexpressing bone marrow, biological rep3


title: CCAT2-GT overexpressing bone marrow, biological rep3


title: WT bone marrow, biological rep3


title: CCAT2-GT overexpressing bone marrow, biological rep4


title: normal_control3

value: normal tissue adjacent to tumor


title: WT DC +LPS 24h (mature DC))

description: cultured primary cells


title: normal_control2


title: normal_control1


title: WT, LPS+Dex, 1h [WT_LD60_14]

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
14_S10_187_WT_LPS_Dex
WT_LD60_14_log2(cpm)

data_processing:
Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500 at the depth of ~60 million reads per sample. Basecal was performed using CASAVA 1.8. Read quality was evaluated using FASTQC.
50-bp paired reads were mapped to annotated mouse genome (mm10, build 38.75, 41,128 genes and 87,108 transcripts) with CLC Bio Genomic Workbench 7.5 software (Qiagen). Duplicated reads with more than 5 copies were discarded
Read count table containing unique exon reads was analyzed using EdgeR package to determine differentially expressed genes. Read counts were scale normalized using the weighted trimmed mean method and expressed as log-transformed counts per million (cpm). All genes with unadjusted p-value <0.01 (p<0.05 for NELF-B KO experiment) and fold change >1.5 in at least one pairwise comparison were considered to be differentially expressed and were selected for further analysis.
The average insert size was estimated using bbtools as following bbmerge-auto.sh in1=r1.fastq in2=r2.fastq ihist=ihist.txt extend2=75
Genome_build: mm10, build 38.75
Supplementary_files_format_and_content: comma separated values, containing the expression values (log2cpm, EDGE_R FDR corrected p values), for in vitro differentiated macrophages

molecule: polyA RNA

growth_protocol: C57BL/6 mice (NCI, Charles River Laboratories) and their transgenic derivatives below were maintained in the Hospital for Special Surgery Animal Facility in full compliance with institutional guidelines approved by the HSS Animal Care and Use Committee. The  LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) strains and their handling were previously described

extract_protocol:
Total RNA was isolated using QIAgen RNAeasy kit
Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TrueSeq mRNA-Seq sample preparation kit (Illumina). Quality control of RNA and libraries was performed using the BioAnalyzer 2100. Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.

treatment_protocol: 8-wk old mice were maintained on a regular chow. BMMΦ were isolated and cultured as priviously described.  BMMΦ incubated for 1 h with or without LPS(10 ng/ml) and LPS+Dex (10 ng/ml + 100nm) immidiately prior RNA isolation.

tag: strain background

tag: Sex

value: male

tag: age

value: 8 weeks

value: LysM-Cre:NELF-B wt/wt

value: Bone Marrow derived macrophages (BMDMs)

value: LPS+Dex for 1h


title: KO, LPS, 1h [KO_L60_.5]

description:
5_S4_186_KO_LPS_1h
KO_L60_.5_log2(cpm)

value: LysM-Cre:NELF-B fl/fl

value: LPS for 1h


title: WT, LPS+Dex, 1h [WT_LD60_38]

description:
38_112_WT_LPS_Dex_1h
WT_LD60_38_log2(cpm)


title: WT, LPS, 1h [WT_L60_37]

description:
37_112_WT_LPS_1h
WT_L60_37_log2(cpm)


title: KO, LPS, 1h [KO_L60_61]

description:
61_3_81_6_185_KO_LPS_1h
KO_L60_61_log2(cpm)


title: NELF B KO,untreated control [KO_CO_58]

description:
58_3_8_16_185_KO_control
KO_CO_58_log2(cpm)

source_name: NELF B KO_untreated control

value: none (untreated control)


title: WT, LPS, 1h [WT_L60_77]

description:
77_198_WT_LPS_1h
WT_L60_77_log2(cpm)


title: KO, LPS+Dex, 1h [KO_LD60_62]

description:
62_3_8_16-2_185_KO_LPS_Dex_1h
KO_LD60_62_log2(cpm)


title: WT, LPS+Dex, 1h [WT_LD60_78]

description:
78_198_WT_LPS_Dex_1h
WT_LD60_78_log2(cpm)


title: KO, LPS, 1h [KO_L60_29]

description:
29_2_17_16-2_127_KO_LPS_1h
KO_L60_29_log2(cpm)


title: KO, LPS+Dex, 1h [KO_LD60_30]

description:
30_2_17_16-2_127_KO_LPS_Dex_1h
KO_LD60_30_log2(cpm)


title: KO, LPS+Dex, 1h [KO_LD60_.6]

description:
6_S5_186_KO_LPS_Dex_1h
KO_LD60_.6_log2(cpm)


title: NELF B KO,untreated control [KO_CO_26]

description:
26_2_17_16-2_127_KO_control
KO_CO_26_log2(cpm)


title: WT,untreated control [WT_CO_74]

description:
74_198_WT_control
WT_CO_74_log2(cpm)

source_name: WT_untreated control


title: WT, LPS, 1h [WT_L60_13]

description:
13_S9_187_WT_LPS_1h
WT_L60_13_log2(cpm)


title: WT,untreated control [WT_CO_34]

description:
34_2_17_16-2_112_WT_control
WT_CO_34_log2(cpm)


title: Isthmic organizer like cell 1

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

description:
IsO 1
replicate 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Human embryonic stem cells

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: Human ESCs (H9, WiCell Inc., Madison, WI, USA) were cultured in human ESC medium composed of DMEM/F12 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 20% Knockout-Serum Replacement (Invitrogen), 1% non-essential amino acid (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma, St. Louis, MO, USA), and 4 ng/ml of basic FGF (Peprotech, Rocky Hill, NJ, USA).

extract_protocol: Total RNA was isolated using Easy-Spin Total RNA Extraction Kit (iNtRON Biotechnology, Sungnam, Kyungki-do, Korea). cDNA was synthesized from 1 µg of total RNA using PrimeScript RT Master Mix (Takara Bio, Kusatsu, Shiga, Japan).

treatment_protocol: For differentiation, embryoid bodies (EBs) were formed by mechanically detaching ESC colonies and culturing them in DMEM/F12:Neurobasal media (Invitrogen) (1:1), 1% N2 supplement (Invitrogen), and 2% B27 supplement without vitamin A (Invitrogen). On day 4 of differentiation, these EBs were plated onto Matrigel (BD Biosciences, Bedford, MA, USA)-coated dishes and cultured in the same medium except that the concentration of N2 supplement was reduced by half (0.5%) for five days. During the first 4 days, 5 μM dorsomorphin (Calbiochem, San Diego, CA, USA) and 10 μM SB431542 (SB) (Sigma) were added into the medium to facilitate neural induction. To induce IsO-like cells, CHIR99021 (CHIR) at various concentrations (0 – 1.2 µM) (Calbiochem) and 100 ng/ml FGF8 (Peprotech) were added into the medium.

value: Isthmic organizer like cell


title: control neural cell 1

description:
Control 1
replicate 1

value: control neural cell


title: control neural cell 2

description:
Control 2
replicate 2


title: control neural cell 3

description:
Control 3
replicate 3


title: Isthmic organizer like cell 2

description:
IsO 2
replicate 2


title: Isthmic organizer like cell 3

description:
IsO 3
replicate 3


title: Rd1_selection_rep1

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

library_source: genomic

data_processing:
The occurrence of sgRNAs indexes were summarized with the Bioconductor Biostrings package (PDict class)
Enriched genes were identified via MAGeCK, a Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout method for prioritizing single-guide RNAs, genes, and pathways in genome-scale CRISPR/Cas9 knockout screens
Genome_build: Human GeCKO v2 half-library A (can be used in either 1- or 2-plasmid systems)
Supplementary_files_format_and_content: tab-delimited text files, csv and excel files include the occurrence of each sgRNA indexes in Library A for each sample separately

growth_protocol: A549 cells were cultured in standard conditions: passaged every 48hr in DMEM containing 10% fetal bovine serum and 1% penicilin/streptomycin

extract_protocol:
Genomic DNA was extracted using the Blood and Cell Culture Maxi Kit or Mini Kit (Qiagen)
Genomic DNA from naïve cells or cells surviving lethal H5N1 infection was extracted. The integrated sgRNA cassette was PCR amplified from genomic DNA. Illumina barcodes were incorporated in the PCR primers.

treatment_protocol: A549 cells were transduced with sgRNA lentivirus and infected with low pathogenic H5N1 virus

tag: cell line background

value: Human lung epithelial cells

value: A549-GeCKO; pooled library of A549 cells lacking individual gene

tag: subjected to

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 1 (Replicate 1)


title: Rd2_selection_rep2

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 2 (Replicate 2)


title: Rd5_selection_rep2

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 5 (Replicate 2)


title: Rd4_selection_rep1

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 4 (Replicate 1)


title: Rd3_selection_rep2

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 3 (Replicate 2)


title: Rd4_selection_rep2

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 4 (Replicate 2)


title: Rd3_selection_rep1

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 3 (Replicate 1)


title: Rd1_selection_rep2

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 1 (Replicate 2)


title: PDVt  NS 6h

city: POITIERS

first: Marie

last: Simonneau

address: 1 RUE GEORGES BONNET

country: France

institute: LITEC EA4331

description: murine transformed keratinocytes

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Transfer 120 μl of hyb solution containing fragmented and labeled DNA to each well, then place the hybridation tray with the arry strip into a clamp inside the hybridation station. • Hybridize 16 hours at 48° in Affymetrix Hybridization Station• Fluidics washing is the GeneAtlasTM Fluidics Station.

scan_protocol: Affymetrix GeneAtlasTM Imaging Station

data_processing: Data were processed using Expression Console software.

source_name: PDVC57 cells - Non stimulated - 6 hours

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: PDVC57 cell line

extract_protocol: Total RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instruction.

treatment_protocol: Cells were cultured in DMEM-F12 medium 0,1% FBS with or without murine rOSM (10ng/mL) for 6h or 24h.

value: keratinocyte


title: PDVt  NS 24h

description: murine transformed keratinocytes

source_name: PDVC57 cells - Non stimulated - 24 hours


title: PDVt  OSM 24h

description: murine transformed keratinocytes

source_name: PDVC57 cells - OSM treated - 24 hours


title: Mixture of H2228, H1975 and HCC827 human lung cancer cell lines in equal proportion

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Fastq files were generated using Cellranger. All R1 files were concatenated and all R2 files were concatenated for processing with scPipe.
Sample filtered gene count matrix was generated using scPipe with ENSEMBL GRCh38p10 gene annotation. With scPipe, we processed the 4000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells.
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: gene_count.csv:  Counts matrix with samples along the columns and genes along the rows
Supplementary_files_format_and_content: index_anno.csv: 4001 most abundant cell barcodes with cell ids, barcode sequence and counts

growth_protocol: The cell lines H2228, NCI-H1975 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin. The cells were grown independently at 37˚C with 5% carbon dioxide until near 100% confluency.

extract_protocol:
Cells were PI stained and 120,000 live cells were sorted for each cell line by FACS to acquire an accurate equal mixture of live cells from the three cell lines. This mixture was then processed by the 10X Genomics Chromium single cell platform using the manufacturer’s 3' protocol to obtain a pooled library.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The library was prepared for sequencing using an Illumina 150 cycle (v2 chemistry) high output kit and sequenced on an Illumina Nextseq 500 to obtain paired-end reads.

value: Human lung adenocarcinoma cell line

tag: barcode coordinate

value: bases 1 to 16 of R1

tag: umi coordinate

value: bases 17 to 26 of R1


title: PDVt OSM 6h

description: murine transformed keratinocytes

source_name: PDVC57 cells - OSM treated - 6 hours


title: Rd5_selection_rep1

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 5 (Replicate 1)


title: Rd2_selection_rep1

value: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 2 (Replicate 1)


title: N5

city: London

first: Hristina

middle: Chavdarova

last: Vasileva

state: London

address: Keppel Street

department: CRD

country: United Kingdom

institute: LSHTM

description:
Solomon Islands child
SB005203
Conjunctival gene expression data from Solomon Islands children without TF or Ct

hyb_protocol: cDNA was hybridised to GeneChip HTA 2.0 microarrays according to the NuGEN Hybridization, Cocktail Assembly and Fluidics Protocol

scan_protocol: GeneChip scanner was used for signal detection. Obtained probe sets hybridization intensities row data for each sample was stored in CEL files, using Affimetrix Launcher

data_processing: Raw hybridisation intensities were normalised using RMA algorithm and annotated with GENBANK accession numbers using Affimetrix hta20 annotation. Probe sets lacking hybridization intensities and/or accession number, those redundent per gene and GeneChip endogenous controls, were discarted from overal data. Probe sets with interquirtile range lower than 0.1log2 were discarded.

source_name: Human Tarsal Conjunctiva

label_protocol: cDNA fragmentation and labelling was performed according to FL-Ovation cDNA Biotin Module V2 protocol using fragmentation enzyme and biotin for cDNA labelling. The final volume obtained was 50µL of cDNA per sample.

extract_protocol: Total RNA from each sample was extracted using Qiagen AllPrep Mini protocol. 25uL cDNA was generated from RNA template using NuGEN Ovation Pico WTA System V2 protocol

tag: gender

value: female

value: 3 years old

tag: phenotype

value: no TF or Ct

tag: tissue

value: conjunctiva


title: N6

description:
Solomon Islands child
SB009823
Conjunctival gene expression data from Solomon Islands children without TF or Ct

value: 5 years old


title: D5

description:
Solomon Islands child
SB001584
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection

value: 6 years old

value: trachomatous inflammation-follicular (TF) and no Ct


title: N3

description:
Solomon Islands child
SB001595
Conjunctival gene expression data from Solomon Islands children without TF or Ct

value: male

value: 2 years old


title: D7

description:
Solomon Islands child
SB005071
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection

value: 9 years old


title: D4

description:
Solomon Islands child
SB005698
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection


title: N2

description:
Solomon Islands child
SB003641
Conjunctival gene expression data from Solomon Islands children without TF or Ct


title: D6

description:
Solomon Islands child
SB000539
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection


title: N7

description:
Solomon Islands child
SB001760
Conjunctival gene expression data from Solomon Islands children without TF or Ct


title: N1

description:
Solomon Islands child
SB004917
Conjunctival gene expression data from Solomon Islands children without TF or Ct

value: 7 years old


title: T_Lymph_P9

data_processing:
Fastq files were concatenated together and mapped using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the sc_gene_counting function from the scPipe package  (Tian et al. 2017 https://www.biorxiv.org/content/early/2017/08/14/175927) with the ENSEMBL v86 mouse annotation.
Genome_build: NCBI Build 38 patch 4
Supplementary_files_format_and_content: gene_count.csv

source_name: Sorted blood

extract_protocol:
B lymphocytes (B220+ FSC-Alow), erythroblasts (Ter119+ CD44+, FSC-Amid/high), granulocytes (Mac1+ Gr1+) and high-end progenitor/stem (Lin- Kit+ Sca1+) were sorted from the bone marrow of a C57BL/6 10-13weeks old female. T cells (CD3+ FSC-Alow) were isolated from the thymus of the same mouse. Bone marrow and thymus were dissociated mechanically, washed and stained with antibodies for 1hr on ice. Single cells were deposited on a 384 well plate using an Aria cell sorter (Beckman). Index data was collected. Single cells were indexed sorted into 384 well plate format directly into lysis buffer as adapted from Celseq2 protocol
CelSeq2 (adapted at WEHI), barcode sequences are in bases 1 to 6 in read 1 and UMI sequences are in bases 7 to 14 in read 1.

tag: cell type

tag: barcode sequence

value: CTACGAAC

value: 1 to 6 in R1

value: 7 to 14 in R1

tag: fsc-a

tag: fsc-h

tag: ssc-a

tag: time

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg

tag: apc ter119

tag: cd3 al700

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450

tag: b220 apc cy7


title: T_Lymph_P8

value: GAGAGAAG

tag: umi coordinate

tag: barcode coordinate


title: T_Lymph_P4

tag: cell type

value: TACAGCGT


title: T_Lymph_P10

tag: barcode sequence

value: AACACCAC


title: T_Lymph_P7

value: TGCAGACT

tag: fsc-a


title: T_Lymph_P3

value: ACGCCATA

tag: fsc-h


title: T_Lymph_P6

value: TAGGCCAT

tag: ssc-a


title: D2

description:
Solomon Islands child
SB004158
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection

tag: gender

value: female

tag: age

value: 4 years old

tag: phenotype

tag: tissue

value: conjunctiva


title: T_Lymph_P12

value: ACACTCGA

tag: time

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg

tag: apc ter119


title: T_Lymph_P5

value: GGTGATTC

tag: cd3 al700

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450

tag: b220 apc cy7


title: D3

description:
Solomon Islands child
SB005577
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection

value: male

value: trachomatous inflammation-follicular (TF) and no Ct


title: D1

description:
Solomon Islands child
SB010725
Conjunctival gene expression data from Solomon Islands children with TF without Ct infection

value: 9 years old


title: DI6

description:
Solomon Islands child
SB008107
Conjunctival gene expression data from Solomon Islands children with TF and Ct

value: ocular Chlamydia trachomatis (Ct) infection and trachomatous inflammation-follicular (TF)


title: DI3

description:
Solomon Islands child
SB011836
Conjunctival gene expression data from Solomon Islands children with TF and Ct


title: DI2

description:
Solomon Islands child
SB012441
Conjunctival gene expression data from Solomon Islands children with TF and Ct

value: 7 years old


title: DI5

description:
Solomon Islands child
SB002563
Conjunctival gene expression data from Solomon Islands children with TF and Ct

value: 6 years old


title: DI1

description:
Solomon Islands child
SB013112
Conjunctival gene expression data from Solomon Islands children with TF and Ct


title: DI4

description:
Solomon Islands child
SB002739
Conjunctival gene expression data from Solomon Islands children with TF and Ct

value: 3 years old


title: T_Lymph_P11

tag: cell type

tag: barcode sequence

value: ACGTATCG

tag: umi coordinate

value: 1 to 6 in R1

tag: barcode coordinate

value: 7 to 14 in R1

tag: fsc-a


title: N4

description:
Solomon Islands child
SB009746
Conjunctival gene expression data from Solomon Islands children without TF or Ct

tag: gender

tag: age

value: 5 years old

tag: phenotype

value: no TF or Ct


title: T_Lymph_P14

value: GCTTGATG

tag: fsc-h

tag: ssc-a

tag: time

tag: fitc cd44


title: T_Lymph_P16

value: CTGGTATG

tag: pcp cy55 c-kit

tag: fg

tag: apc ter119

tag: cd3 al700


title: T_Lymph_O19

value: TCCAGTGA

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450

tag: b220 apc cy7


title: T_Lymph_O17

tag: cell type

tag: barcode sequence

value: GAATCCAC

tag: umi coordinate

tag: barcode coordinate


title: T_Lymph_O20

value: CGCAATAC

tag: fsc-a


title: T_Lymph_O14

value: GAGACCTT

tag: fsc-h


title: T_Lymph_O21

value: AGTGTCTG

tag: ssc-a


title: T_Lymph_O22

value: CAACTAGC

tag: time


title: T_Lymph_P15

value: TCGAGACT

tag: fitc cd44


title: T_Lymph_P13

value: GTACATCG

tag: pcp cy55 c-kit


title: T_Lymph_O24

value: TAGGCTGT

tag: fg


title: T_Lymph_P17

value: GTCACGTA

tag: apc ter119


title: T_Lymph_O11

value: GTGAGTTC

tag: cd3 al700


title: T_Lymph_O10

value: GGTCCAAT

value: 1 to 6 in R1

tag: gr1 pe


title: T_Lymph_P19

value: TCAGCGTA

value: 7 to 14 in R1

tag: pe-cy7 sca-1


title: T_Lymph_P20

value: AGAAGAGG

tag: mac-1 ef450


title: T_Lymph_O6

value: CCACTAAG

tag: b220 apc cy7


title: T_Lymph_O9

tag: cell type

value: GGCTATCA


title: T_Lymph_O15

tag: barcode sequence

value: AGCTCATG


title: T_Lymph_O13

value: GGAAGAAG

tag: umi coordinate


title: T_Lymph_O18

value: CGTCGATA

tag: barcode coordinate


title: T_Lymph_O16

value: CTCACAGA

tag: fsc-a


title: T_Lymph_O23

value: ATACCACG

tag: fsc-h


title: T_Lymph_O5

value: TCACACGA

tag: ssc-a


title: T_Lymph_P21

value: TATCCGGA

tag: time


title: T_Lymph_O2

value: GCCATGAT

tag: fitc cd44


title: LSK_N3

value: LSK

value: GGACTTGT

tag: pcp cy55 c-kit


title: T_Lymph_O7

value: TACCGTGA

tag: fg


title: T_Lymph_O8

value: GCCATCAA

value: 1 to 6 in R1

tag: apc ter119


title: T_Lymph_O4

value: AGCACTTG

value: 7 to 14 in R1

tag: cd3 al700


title: T_Lymph_O3

value: ATTGTGGC

tag: gr1 pe


title: LSK_N1

value: GCGCTTAA

tag: pe-cy7 sca-1


title: LSK_N11

value: CAGTACCA

tag: mac-1 ef450


title: LSK_N5

value: ACCGTGAT

tag: b220 apc cy7


title: LSK_N2

tag: cell type

value: GTTACCGA


title: T_Lymph_O1

tag: barcode sequence

value: CTCAAGAC


title: LSK_N13

value: TGCTAGGT

tag: umi coordinate


title: LSK_N17

value: GTCAGTAC

tag: barcode coordinate


title: LSK_N18

value: CAATCGGT

tag: fsc-a


title: LSK_N6

value: ATGCAGTC

tag: fsc-h


title: LSK_N4

value: LSK

value: TGACCATG

tag: ssc-a


title: LSK_N7

value: CGTAGTGT

tag: time


title: LSK_N21

value: GTTGAGTC

tag: fitc cd44


title: T_Lymph_P18

value: ACGTGTGT

value: 1 to 6 in R1

tag: pcp cy55 c-kit


title: LSK_N20

value: GCATGTGT

value: 7 to 14 in R1

tag: fg


title: LSK_N9

value: TGGTTGCA

tag: apc ter119


title: T_Lymph_O12

value: ATGGTCCA

tag: cd3 al700


title: LSK_M22

value: TAGCGTCA

tag: gr1 pe


title: LSK_N10

value: TAGCCGAT

tag: pe-cy7 sca-1


title: LSK_N12

value: CAATTGGC

tag: mac-1 ef450


title: LSK_N8

value: AGGTTCAC

tag: b220 apc cy7


title: LSK_N14

tag: cell type

value: AACGTCAC


title: LSK_M20

tag: barcode sequence

value: GCCAATTG


title: LSK_N19

value: GCGTGTAT

tag: umi coordinate


title: LSK_M14

value: LSK

value: TAAGCTGC

tag: barcode coordinate


title: LSK_N15

value: CCGATGTA

tag: fsc-a


title: LSK_M15

value: AGCGTATC

tag: fsc-h


title: LSK_N23

value: GTATGGTC

tag: ssc-a


title: LSK_M24

value: AGCATGTC

value: 1 to 6 in R1

tag: time


title: LSK_M10

value: GATTGGTC

value: 7 to 14 in R1

tag: fitc cd44


title: LSK_N22

value: CACTACAG

tag: pcp cy55 c-kit


title: LSK_N24

value: TCGCTGAA

tag: fg


title: LSK_M16

value: ATTGCCGA

tag: apc ter119


title: LSK_M7

value: ACTCTGAG

tag: cd3 al700


title: LSK_N16

value: GGTTAGCT

tag: gr1 pe


title: LSK_M8

value: GGCCAATT

tag: pe-cy7 sca-1


title: LSK_M9

value: CATTGTGG

tag: mac-1 ef450


title: LSK_M18

value: TGGCAACT

tag: b220 apc cy7


title: LSK_M23

tag: cell type

value: LSK

value: ACCAAGCT


title: LSK_M3

tag: barcode sequence

value: TCAAGCAC


title: LSK_M21

value: TGCCAGAT

tag: umi coordinate


title: LSK_M11

value: TCAGGCAT

tag: barcode coordinate


title: LSK_M6

value: ATGTCCAG

tag: fsc-a


title: LSK_M13

value: GACATGCT

value: 1 to 6 in R1

tag: fsc-h


title: LSK_M17

value: TAGGTTGC

value: 7 to 14 in R1

tag: ssc-a


title: LSK_L5

value: TCGCACAA

tag: time


title: LSK_L8

value: TGGTGATC

tag: fitc cd44


title: LSK_L9

value: CGATAGCT

tag: pcp cy55 c-kit


title: LSK_L1

value: CTAGGATC

tag: fg


title: LSK_L11

value: CGCTAGTA

tag: apc ter119


title: LSK_L3

value: TGCGGATT

tag: cd3 al700


title: LSK_L2

value: ACACGCAT

tag: gr1 pe


title: LSK_M4

value: LSK

value: GCAAGTTC

tag: pe-cy7 sca-1


title: LSK_L4

value: CGACCATA

tag: mac-1 ef450


title: LSK_M12

value: TGCGGTTA

tag: b220 apc cy7


title: LSK_L15

tag: cell type

value: CAACATGC


title: LSK_L7

tag: barcode sequence

value: GAACTTCG


title: LSK_L20

value: CACACTAG

tag: umi coordinate


title: LSK_M1

value: GTCATGCA

value: 1 to 6 in R1

tag: barcode coordinate


title: LSK_L6

value: AGCTGTTG

value: 7 to 14 in R1

tag: fsc-a


title: LSK_L12

value: CGCAACAT

tag: fsc-h


title: LSK_L14

value: AGGAAGGA

tag: ssc-a


title: LSK_L13

value: GACCTACA

tag: time


title: LSK_M5

value: GGTATCGT

tag: fitc cd44


title: LSK_L16

value: CCAATAGC

tag: pcp cy55 c-kit


title: LSK_L10

value: ATCCGCAA

tag: fg


title: LSK_M2

value: LSK

value: GGTACACT

tag: apc ter119


title: LSK_L17

value: TCGAGTTG

tag: cd3 al700


title: LSK_K23

value: CGTGATGT

tag: gr1 pe


title: LSK_K22

value: ACCAAGTC

tag: pe-cy7 sca-1


title: LSK_L19

value: ACCATGTG

tag: mac-1 ef450


title: LSK_K21

value: CGTAGCAT

tag: b220 apc cy7


title: LSK_K19

tag: cell type

value: AGTATCCG


title: LSK_L21

tag: barcode sequence

value: TGCAATGC

value: 1 to 6 in R1


title: LSK_K18

value: GTGGTCTA

tag: umi coordinate

value: 7 to 14 in R1


title: LSK_K15

value: ACGCACTA

tag: barcode coordinate


title: LSK_K24

value: CCATCGAA

tag: fsc-a


title: LSK_L23

value: TGGTCTGA

tag: fsc-h


title: LSK_K20

value: TATTGCGG

tag: ssc-a


title: LSK_K16

value: AGTCATGC

tag: time


title: LSK_K14

value: LSK

value: AACTGTGC

tag: fitc cd44


title: LSK_L24

value: GTCATGTG

tag: pcp cy55 c-kit


title: LSK_L18

value: GCGCAATT

tag: fg


title: LSK_K17

value: TGTATGGC

tag: apc ter119


title: LSK_K11

value: TGCATGGT

tag: cd3 al700


title: LSK_K12

value: GCAGTCAT

tag: gr1 pe


title: LSK_L22

value: GCAATGTC

tag: pe-cy7 sca-1


title: LSK_K13

value: ACTACGGT

tag: mac-1 ef450


title: LSK_K7

value: ACTTCAGG

value: 1 to 6 in R1

tag: b220 apc cy7


title: LSK_K10

tag: cell type

value: CAAGTGTC

value: 7 to 14 in R1


title: LSK_K9

tag: barcode sequence

value: GCTCTGAA


title: LSK_K4

value: TCTCAAGG

tag: umi coordinate


title: LSK_K2

value: ACCAACGT

tag: barcode coordinate


title: LSK_K5

value: TATGGCCA

tag: fsc-a


title: LSK_K3

value: LSK

value: GTAGTGTC

tag: fsc-h


title: Grans_J2

value: Grans

value: CAAGACTC

tag: ssc-a


title: Grans_J1

value: CACTGCAA

tag: time


title: LSK_K1

value: TCTCCTCT

tag: fitc cd44


title: Grans_J4

value: GGTGCATT

tag: pcp cy55 c-kit


title: Grans_J5

value: GTGTGGTT

tag: fg


title: Grans_J3

value: GTGCTCAA

tag: apc ter119


title: LSK_K8

value: ACCACTGA

tag: cd3 al700


title: Grans_J9

value: TACCGAAC

value: 1 to 6 in R1

tag: gr1 pe


title: Grans_J11

value: CGACCTAA

value: 7 to 14 in R1

tag: pe-cy7 sca-1


title: Grans_J6

value: GCCAACTA

tag: mac-1 ef450


title: Grans_J20

value: CTCCTCTT

tag: b220 apc cy7


title: Grans_J17

tag: cell type

value: CTAACACG


title: Grans_J13

tag: barcode sequence

value: CAGACGTT


title: Grans_J8

value: CTACGACA

tag: umi coordinate


title: Grans_J16

value: Grans

value: TCATGGTG

tag: barcode coordinate


title: Grans_J14

value: CGAATCCA

tag: fsc-a


title: LSK_K6

value: LSK

value: TACACGTG

tag: fsc-h


title: Grans_J19

value: GCGTTAGT

tag: ssc-a


title: Grans_J23

value: TATGGCTG

tag: time


title: Grans_J22

value: GACCACTA

tag: fitc cd44


title: Grans_I22

value: ATTGCTGG

tag: pcp cy55 c-kit


title: Grans_J12

value: CTGTGAGT

value: 1 to 6 in R1

tag: fg


title: Grans_I23

value: TCGACCAA

value: 7 to 14 in R1

tag: apc ter119


title: Grans_I24

value: CGTAACTG

tag: cd3 al700


title: Grans_J21

value: CGCATGAT

tag: gr1 pe


title: Grans_I18

value: GCAAGCTT

tag: pe-cy7 sca-1


title: Grans_J24

value: GCATGTAC

tag: mac-1 ef450


title: Grans_J18

value: Grans

value: TCTTCCTC

tag: b220 apc cy7


title: Grans_J7

tag: cell type

value: TACTGTGG


title: Grans_J15

tag: barcode sequence

value: TCCATGAG


title: Grans_I15

value: AGCCTAAC

tag: umi coordinate


title: Grans_J10

value: AGGCCATT

tag: barcode coordinate


title: Grans_I16

value: CTAAGCCA

tag: fsc-a


title: Grans_I12

value: ATGCAGCT

tag: fsc-h


title: Grans_I5

value: AGCAACTC

tag: ssc-a


title: Grans_I9

value: CTATAGGC

tag: time


title: Grans_I10

value: AAGCTCCA

value: 1 to 6 in R1

tag: fitc cd44


title: Grans_I8

value: ATCTACGG

value: 7 to 14 in R1

tag: pcp cy55 c-kit


title: Grans_I13

value: AACCGTAC

tag: fg


title: Grans_I4

value: TACGGATC

tag: apc ter119


title: Grans_I17

value: AAGGAGGA

tag: cd3 al700


title: Grans_I14

value: Grans

value: CTCTCTCT

tag: gr1 pe


title: Grans_I21

value: GTGACACT

tag: pe-cy7 sca-1


title: Grans_I11

value: CAATCCAG

tag: mac-1 ef450


title: Grans_H3

value: CGAATCGT

tag: b220 apc cy7


title: Grans_H1

tag: cell type

value: TGCACTGA


title: Grans_I19

tag: barcode sequence

value: CACAGTAC


title: Grans_H8

value: GGAACTCT

tag: umi coordinate


title: Grans_I7

value: ACAGCACT

tag: barcode coordinate


title: Grans_I6

value: AAGTCGCT

tag: fsc-a


title: Grans_I20

value: ATGCACCA

tag: fsc-h


title: Grans_I3

value: CTAGACCA

value: 1 to 6 in R1

tag: ssc-a


title: Grans_I2

value: CACAATCG

value: 7 to 14 in R1

tag: time


title: Grans_I1

value: ATTGGCGT

tag: fitc cd44


title: Grans_H22

value: CCTTCTTC

tag: pcp cy55 c-kit


title: Grans_H6

value: Grans

value: GTAACGCT

tag: fg


title: Grans_H19

value: GGAGTCTT

tag: apc ter119


title: Grans_H14

value: TAGTCAGC

tag: cd3 al700


title: Grans_H7

value: CGAACACT

tag: gr1 pe


title: Grans_H5

value: AGTTGCTG

tag: pe-cy7 sca-1


title: Grans_G24

value: ACAGCTAC

tag: mac-1 ef450


title: Grans_H12

value: CAGTCCAA

tag: b220 apc cy7


title: Grans_H21

tag: cell type

value: ACGAACTC


title: Grans_H9

tag: barcode sequence

value: AGTCGTAC


title: Grans_H2

value: GTTGCGAT

tag: umi coordinate


title: Grans_H17

value: CATGGTTG

tag: barcode coordinate


title: Grans_H10

value: ACGGTTAC

value: 1 to 6 in R1

tag: fsc-a


title: Grans_H18

value: GCGTTGTA

value: 7 to 14 in R1

tag: fsc-h


title: Grans_H11

value: ATTGGCAC

tag: ssc-a


title: Grans_H4

value: Grans

value: GTGCATGT

tag: time


title: Grans_H23

value: CATACGTG

tag: fitc cd44


title: Grans_H24

value: ACATTGGC

tag: pcp cy55 c-kit


title: Grans_H15

value: ACGACATC

tag: fg


title: Grans_H20

value: AACGCTGT

tag: apc ter119


title: Grans_H13

value: TCCTTCTC

tag: cd3 al700


title: Grans_G23

value: GGCTTAAC

tag: gr1 pe


title: Grans_G19

value: GTACGACT

tag: pe-cy7 sca-1


title: Grans_H16

value: GTTGTCAG

tag: mac-1 ef450


title: Grans_G13

value: GGTCAATC

tag: b220 apc cy7


title: Grans_G21

tag: cell type

value: ATAGCGTC


title: Grans_G18

tag: barcode sequence

value: CGATTCAG


title: Grans_G17

value: GCTACAAC

tag: umi coordinate

value: 1 to 6 in R1


title: Grans_G14

value: TGTCGATG

tag: barcode coordinate

value: 7 to 14 in R1


title: Grans_G9

value: Grans

value: GATTCGGT

tag: fsc-a


title: Grans_G16

value: AATCCGCA

tag: fsc-h


title: Grans_G3

value: CGAACTGT

tag: ssc-a


title: Grans_G20

value: CGACATAC

tag: time


title: Grans_G11

value: GTTGTGAC

tag: fitc cd44


title: Grans_G15

value: CCAACTAG

tag: pcp cy55 c-kit


title: EryB_F1

value: EryB

value: ATTCGCAG

tag: fg


title: EryB_F2

value: TAACCGTG

tag: apc ter119


title: Grans_G8

value: GTAGGTCT

tag: cd3 al700


title: EryB_F5

value: ATAGGCTC

tag: gr1 pe


title: Grans_G12

value: GTGTAGCT

tag: pe-cy7 sca-1


title: Grans_G10

value: TGGCATCA

tag: mac-1 ef450


title: Grans_G7

value: GAATCGTC

value: 1 to 6 in R1

tag: b220 apc cy7


title: Grans_G5

tag: cell type

value: ACCGTTAG

value: 7 to 14 in R1


title: EryB_F8

tag: barcode sequence

value: CGACGTAT


title: EryB_F3

value: AGGAGGAA

tag: umi coordinate


title: EryB_F9

value: ACATGCCA

tag: barcode coordinate


title: EryB_F13

value: TACCGATG

tag: fsc-a


title: EryB_F15

value: AGCTTACG

tag: fsc-h


title: Grans_G22

value: Grans

value: AACCAGTC

tag: ssc-a


title: Grans_G6

value: CCGATAGT

tag: time


title: Grans_G2

value: CACGAGTT

tag: fitc cd44


title: EryB_F19

value: EryB

value: ACACACGT

tag: pcp cy55 c-kit


title: EryB_F22

value: TGCCAGTA

tag: fg


title: EryB_F7

value: ACACAGCT

tag: apc ter119


title: EryB_F24

value: GTAGTCCA

tag: cd3 al700


title: Grans_G1

value: GGCTAATC

value: 1 to 6 in R1

tag: gr1 pe


title: Grans_G4

value: GATTCGCA

value: 7 to 14 in R1

tag: pe-cy7 sca-1


title: EryB_F4

value: GTCGCTAA

tag: mac-1 ef450


title: EryB_F11

value: GCGTGATT

tag: b220 apc cy7


title: EryB_E18

tag: cell type

value: CACAAGTC


title: EryB_E20

tag: barcode sequence

value: TCGTTGGA


title: EryB_F10

value: GTTCCAAG

tag: umi coordinate


title: EryB_E13

value: TCGACTAG

tag: barcode coordinate


title: EryB_F16

value: GAGTTCCA

tag: fsc-a


title: EryB_E16

value: GTACTGTG

tag: fsc-h


title: EryB_F14

value: EryB

value: TACAGGCT

tag: ssc-a


title: EryB_F6

value: GAGAGGAA

tag: time


title: EryB_E12

value: CGACACAT

tag: fitc cd44


title: EryB_F17

value: GCTGCATA

tag: pcp cy55 c-kit


title: EryB_F21

value: GTAGACCT

tag: fg


title: EryB_F18

value: TACCACGA

value: 1 to 6 in R1

tag: apc ter119


title: EryB_E9

value: AGTGACTC

value: 7 to 14 in R1

tag: cd3 al700


title: EryB_E10

value: TACGAGTC

tag: gr1 pe


title: EryB_F20

value: CTGCAACA

tag: pe-cy7 sca-1


title: EryB_E22

value: TCTCGGAA

tag: mac-1 ef450


title: EryB_F12

value: TGATGCTG

tag: b220 apc cy7


title: EryB_E6

tag: cell type

value: GTACTTGG


title: EryB_E24

tag: barcode sequence

value: ATCCGTAG


title: EryB_E23

value: CGACTACA

tag: umi coordinate


title: EryB_F23

value: EryB

value: AGCGTTAC

tag: barcode coordinate


title: EryB_D1

value: ACAACGTC

tag: fsc-a


title: EryB_E1

value: TGGTCGAT

tag: fsc-h


title: EryB_E21

value: TGAGTTGC

tag: ssc-a


title: EryB_D2

value: CCATCAAG

tag: time


title: EryB_D3

value: ATTGCGTG

tag: fitc cd44


title: EryB_D4

value: CTACGCAA

value: 1 to 6 in R1

tag: pcp cy55 c-kit


title: EryB_E19

value: CAACTGAC

value: 7 to 14 in R1

tag: fg


title: EryB_D7

value: CATCCAGA

tag: apc ter119


title: EryB_D9

value: CAGTGCTA

tag: cd3 al700


title: EryB_D11

value: GGTAACTC

tag: gr1 pe


title: EryB_D10

value: CGTGAATC

tag: pe-cy7 sca-1


title: EryB_E8

value: AGCTTGCA

tag: mac-1 ef450


title: EryB_E11

value: GTGCGTAT

tag: b220 apc cy7


title: EryB_E17

tag: cell type

value: EryB

value: CGATTGTG


title: EryB_D12

tag: barcode sequence

value: CACTAGCA


title: EryB_E14

value: TCACGGTA

tag: umi coordinate


title: EryB_E15

value: ATGGTGCT

tag: barcode coordinate


title: EryB_D13

value: GATACTGC

tag: fsc-a


title: EryB_D15

value: GGATGCTT

tag: fsc-h


title: EryB_E3

value: TGACTACG

tag: ssc-a


title: EryB_E4

value: GGCATGTT

value: 1 to 6 in R1

tag: time


title: Bim-/- Bmf-/- Anoikis 3

city: Worcester

first: Roger

middle: J

last: Davis

state: MA

address: 373 Plantation St Suite 309

institute: University of Massachusetts Medical School

description: Suspension culture

data_processing:
Paired-end, 40-bp reads from each sample were aligned to the mouse genome (mm10) using TopHat and Bowtie.  Alignments for each sequencing run were merged when read countings was performed.  Gene expression was quantified as fragments per kilobase of exon model per million mapped fragments (FPKM) using Cufflinks version 1.0.3.
Differential expression for attached and suspended Bim-/- Bmf-/- kidney epithelial cells was determined using the Cufflinks tool Cuffdiff.  The criteria for differential expression were: genes with FPKMs ≥ 0.1 in at least one of the tested conditions, whose absolute log2 fold-changes between conditions were ≥ 0.5, and whose FDR-adjusted p-values for significance of differential expression were ≥ 0.05
The processed data file is in the format of Cufflinks output.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is in Cufflinks format and was outputted as a tab-delimited text file that includes RPKM values.

source_name: Kidney epithelial cells

growth_protocol: Bim-/- Bmf-/- kidney epithelial cells isolated from 8 week-old mice were either cultured in attached conditions or suspension culture (4 hrs) before RNA isolation using the RNEasy kit with DNase treatment (Qiagen).

extract_protocol:
Total RNA was extracted from cultured kidney epithelial cells using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  On-column DNA digestion was performed to eliminate genomic DNA.  RNA quality was verified (RNA integrity number >9) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San-Diego, CA) according to the manufacturer’s instructions. An Illumina library was built and sequenced using a HiSeq 2000 (Illumina).

tag: strain

tag: genotype

value: Bim-/- Bmf-/-


title: EryB_D5

value: GCTAAGCT

value: 7 to 14 in R1

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg


title: Bim-/- Bmf-/- Anoikis 2

description: Suspension culture


title: EryB_E2

value: TGCGACTA

tag: apc ter119

tag: cd3 al700

tag: gr1 pe


title: Bim-/- Bmf-/- Anoikis 1

description: Suspension culture


title: EryB_E7

value: TAGGTGCT

tag: pe-cy7 sca-1

tag: mac-1 ef450

tag: b220 apc cy7


title: Bim-/- Bmf-/- Attached 3

description: Attached culture conditions


title: EryB_D6

tag: cell type

tag: barcode sequence

value: ATGCCAGT

tag: umi coordinate


title: EryB_E5

value: ACGATGTC

tag: barcode coordinate

tag: fsc-a

tag: fsc-h


title: EryB_D8

value: EryB

value: GACTACCA

tag: ssc-a

tag: time


title: EryB_D14

value: GTGCGTTA

tag: fitc cd44


title: Bim-/- Bmf-/- Attached 2

description: Attached culture conditions

tag: strain

tag: genotype


title: Bim-/- Bmf-/- Attached 1

description: Attached culture conditions


title: EryB_D18

value: TAGCGATC

tag: pcp cy55 c-kit

tag: fg

tag: apc ter119


title: EryB_D19

value: CCTAGTAG

tag: cd3 al700

tag: gr1 pe

tag: pe-cy7 sca-1


title: EryB_D20

tag: cell type

value: CAGCTTAG

tag: mac-1 ef450

tag: b220 apc cy7


title: EryB_D21

tag: barcode sequence

value: AGGTTCCA

tag: umi coordinate

tag: barcode coordinate


title: EryB_D16

value: TCAGGTGT

tag: fsc-a

tag: fsc-h

tag: ssc-a


title: EryB_D17

value: TAGCTCAG

tag: time

tag: fitc cd44


title: EryB_D24

value: GAAGGAAG

value: 1 to 6 in R1

tag: pcp cy55 c-kit


title: EryB_D22

value: TGGCGATT

tag: fg


title: EryB_D23

value: ACCAATCG

value: 7 to 14 in R1

tag: apc ter119


title: EryB_C24

value: ACTGTGAC

tag: cd3 al700


title: KO_Input_2

city: Beijing

first: Yu

last: Jiang

address: Zhongguancun North Ave

institute: Tsinghua University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.1.2 with the following configurations: -m 1, -S, -q
After alignment, PCR duplicates were removed by picard-tools-1.119 MarkDuplicates
Peaks were called using SICER_V1.1 using SICER.sh with the following settings: Redundancy threshold 1, Window size 200, Fragment size 200, Gap size 600, FDR 1e-7
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER_V1.1. Score represents peak island normalized by library size per million

source_name: Th17 cells cultured in vitro (TGFβ plus IL-6)

growth_protocol: Naïve CD4+T cells were activated with coated anti-CD3 and anti-CD28 and cultured in the presence of TGF-β and IL-6 for 3 days

extract_protocol:
Lysates were prepared following the protocol of Active Motif's ChIP-IT Express Enzymatic Kit (#53035) and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Bioo Scientific's instructions accompanying the NEXTflex Illumina ChIP-Seq Library Prep Kit (#5143).

treatment_protocol: Before harvesting, the cells were restimulated by PMA and ionomycin for 2 hours

value: Th17 cells

tag: strain

tag: genotype

tag: chip antibody


title: KO_H3K27Ac_2

tag: cell type


title: Asxl1-MT-cKI_H2AK119Ub

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

description: H2AK119Ub in KI cells

data_processing:
CHIP-seq was alligned with Bowtie2 peakcall with macs2
RNA-seq was alligned with STAR and quantifcation was done with Sailfish raw counts are stored in the counts file
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw counts Chip-seq bigwig normlized signal

source_name: c-Kit+ Bone Marrow cells

extract_protocol:
Hematopoietic cells were harvested from long bones that were triturated and passed through 40-μm nylon mesh to obtain a single cell suspension. Isolation of c-Kit+ BM cells was performed with anti-CD117 MicroBeads, and separated on a MACS Column in the magnetic field of a MACS Separator (Miltenyi Biotec).
RNA-seq: Library preparation for whole transcriptome analysis was performed according to the manufacturer’s instructions (SureSelect Strand Specific RNA Preparation Kit; Agilent Technologies, Santa Clara, CA, USA). Briefly, poly(A) RNA purified from 2 μg of total RNA was chemically fragmented to appropriate sizes. First-strand cDNA was synthesized from the fragmented poly(A)-selected mRNA, followed by the synthesis of second-strand cDNA. Then, adaptor oligo-DNA was ligated to both ends of the double-stranded cDNA. Libraries were prepared with 12 cycles of PCR amplification of adaptor-ligated cDNA using primers that are complimentary to the adaptors. The libraries were sequenced by GAIIx next-generation sequencer (Illumina, San Diego, CA, USA) using the single-end 36 bp sequencing protocol. The generated sequence tags were mapped onto the murine genomic sequence (mm10; UCSC Genome Browser) and mRNA expression levels were normalized as reads per kilobase per million.
ChIP-seq : For ChIP-seq in murine cells 10 million BM c-Kit+ cells, isolated with anti-mouse c-Kit Biotin (13-1171-85, eBioscience) and Anti-Biotin Microbeads (130-090-485, Miltenyi Biotec), were used. Briefly, cells were fixed in a 1% methanol-free formaldehyde solution and then resuspended in sodium dodecyl sulfate (SDS) lysis buffer. Lysates were sonicated in an E220 focused-ultrasonicator (Covaris) to a desired fragment size distribution of 100–500 base pairs. IP reactions were performed with the following antibodies, each on approximately 500,000 cells as previously described (Krivtsov et al., 2008); Antibodies used for ChIP include anti-H3K4me3 (Cell Signaling 9751S), anti-H3K27me3 (Millipore 07-449), anti-H2AK119Ub (Cell Signaling 8240), anti-Asxl1 (Santa Cruz Biotechnology, sc-85283), and anti-FLAG (Sigma-Aldrich, F1804).  ChIP assays were processed and barcoded library and raw data analysis were performed as previously described (Micol et al., 2017).

tag: antibody

tag: antibody vendor/catalog#

value: Cell Signaling 8240

tag: genotype/variation


title: Control-cKit-BM-si-H3K27me3

description: H3K27me3 in WT cells

value: Millipore 07-449


title: Asxl1-cKI-cKit-BM-si-H3K27me3

description: H3K27me3 in KI cells


title: Asxl1-mu-KI-BM_ASXL1

description: Asxl1 Chip-seq in WT cells

value: Santa Cruz Biotechnology, sc-85283


title: Asxl1-WT-cKit-rnaseq

description: rnaseq in WT cells


title: Asxl1-KI-cKit-rnaseq

description: rnaseq in KI cells


title: Control-cKit-BM-si-H3K4me3

description: H3K4me3 in WT cells

value: Cell Signaling 9751S


title: Asxl1-mu-KI-BM_Input

description: Input Chip-seq in KI cells


title: Asxl1-mu-KI-BM_FLAG

description: Flag Chip-seq in KI cells

value: anti-FLAG

value: Sigma-Aldrich, F1804


title: WT_Input_1


title: KO_H3K27Ac_1


title: Asxl1-cKI-cKit-BM-si-H3K4me3

description: H3K4me3 in KI cells


title: Control-BM_ASXL1

description: Asxl1 Chip-seq in KI cells


title: WT_Input_2


title: B_Lymph_B24

tag: barcode sequence

value: CGCATGTA

tag: umi coordinate

tag: barcode coordinate

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450

tag: b220 apc cy7


title: Control_H2AK119Ub

description: H2AK119Ub in WT cells


title: B_Lymph_B23

value: GTGATTCG

tag: fsc-a

tag: fsc-h

tag: ssc-a

tag: time

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg


title: WT_H3K27Ac_2

tag: cell type

tag: strain

tag: genotype

tag: chip antibody


title: EryB_C23

value: EryB

tag: barcode sequence

value: TCCTCTTC

tag: umi coordinate

tag: apc ter119

tag: cd3 al700


title: WT_H3K27Ac_1


title: EryB_C22

value: GACCATCA

tag: barcode coordinate

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450


title: EryB_C21

value: TGACTCAG

value: 1 to 6 in R1

tag: fsc-a

tag: fsc-h

tag: ssc-a

tag: b220 apc cy7


title: KO_Input_1


title: EryB_C19

value: TGCACGTA

tag: time

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg


title: EryB_C20

tag: cell type

value: GGTTATGC

value: 7 to 14 in R1


title: EryB_C17

tag: barcode sequence

value: CACGGTAT


title: EryB_C18

value: GGCACTTA

tag: umi coordinate


title: EryB_C16

value: AGTCACGT

tag: apc ter119


title: EryB_C14

value: GCTAGTGT

tag: cd3 al700


title: B_Lymph_B2

value: AGTCTTGG

tag: barcode coordinate


title: EryB_C9

value: CATCAAGC

tag: gr1 pe


title: B_Lymph_B1

value: GACTACTG

tag: pe-cy7 sca-1


title: EryB_C7

value: ACTACACG

tag: mac-1 ef450


title: EryB_C2

value: TGTCGCAA

tag: fsc-a


title: B_Lymph_B3

value: AGCAGCTT

tag: fsc-h


title: EryB_C10

value: EryB

value: ACTGTTGG

tag: ssc-a


title: EryB_C13

value: TGCGTAGT

tag: b220 apc cy7


title: EryB_C3

value: GGACTTAC

value: 1 to 6 in R1

tag: time


title: EryB_C15

value: CTCACGAA

tag: fitc cd44


title: EryB_C11

value: TCAGTGCA

value: 7 to 14 in R1

tag: pcp cy55 c-kit


title: B_Lymph_B4

value: TCACAGAC

tag: fg


title: B_Lymph_B6

tag: cell type

value: ATGACTGC


title: EryB_C1

tag: barcode sequence

value: AGTGTGCT


title: EryB_C5

value: ACGCGTTA

tag: umi coordinate


title: EryB_C12

value: GCGATATC

tag: apc ter119


title: B_Lymph_B11

value: CAACGTAC

tag: cd3 al700


title: B_Lymph_B7

value: CTCTCCTT

tag: barcode coordinate


title: B_Lymph_B5

value: CCTGTAAG

tag: gr1 pe


title: B_Lymph_B8

value: CGTGTCAA

tag: pe-cy7 sca-1


title: B_Lymph_B9

value: GCCTTAAG

tag: mac-1 ef450


title: B_Lymph_B10

value: GCACGTAT

tag: fsc-a


title: EryB_C6

value: EryB

value: TACGCTGA

tag: fsc-h


title: B_Lymph_B12

value: GCGTACAT

value: 1 to 6 in R1

tag: ssc-a


title: EryB_C4

value: CTATCGGA

tag: b220 apc cy7


title: EryB_C8

value: ATCACGAC

value: 7 to 14 in R1

tag: time


title: B_Lymph_B13

value: TATCCAGG

tag: fitc cd44


title: B_Lymph_B15

value: GTGTTAGC

tag: pcp cy55 c-kit


title: B_Lymph_B14

value: CCGATATG

tag: fg


title: B_Lymph_B17

tag: cell type

value: GTTGCTGA


title: B_Lymph_B20

tag: barcode sequence

value: ATGCTGAC


title: B_Lymph_A21

value: TAGGTCAC

tag: umi coordinate


title: B_Lymph_A22

value: ACTCAAGC

tag: apc ter119


title: B_Lymph_B21

value: TACTGGCA

tag: cd3 al700


title: B_Lymph_B22

value: CAGTCATG

tag: barcode coordinate


title: B_Lymph_B18

value: CCTGGATA

tag: gr1 pe


title: B_Lymph_B16

value: GTGGTTGT

tag: pe-cy7 sca-1


title: B_Lymph_A19

value: CAACGCTA

tag: mac-1 ef450


title: B_Lymph_A18

value: CCTATGAG

tag: fsc-a


title: B_Lymph_A17

value: GCATTAGC

value: 1 to 6 in R1

tag: fsc-h


title: B_Lymph_A16

value: AGCTCTGA

tag: ssc-a


title: B_Lymph_B19

value: ACCGACAT

value: 7 to 14 in R1

tag: b220 apc cy7


title: B_Lymph_A20

value: GCATAGTC

tag: time


title: B_Lymph_A15

value: ACTTGTGG

tag: fitc cd44


title: B_Lymph_A13

value: CTGCGTAA

tag: pcp cy55 c-kit


title: B_Lymph_A14

value: GTCCAACA

tag: fg


title: B_Lymph_A12

tag: cell type

value: CTCCAAGA


title: B_Lymph_A11

tag: barcode sequence

value: CAAGCCAT


title: mock inoculated leaf at 72 hpi, mo-ei-11 expt, biological replicate 1

city: New Delhi

first: T

middle: R

last: Sharma

state: Delhi

address: Pusa Campus New

country: India

institute: NRCPB

description: gene expression data from mock inoculated rice leaf tissues at 72 hours post inoculation (hpi), Mo-ei-11 experiment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Scanner 3000 (Affymetrix, USA).

data_processing: Data was normalized using GeneChip robust multi-array average (GCRMA) algorithm.

organism: Oryza sativa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The seedlings of susceptible rice cultivar HR-12 were grown under standard physiological conditions of 16 h light and 8 h dark photoperiod at 25 ± 2°C.

extract_protocol: Extraction of total RNA was performed using Spectrum Plant total RNA kit (Sigma)

treatment_protocol: 14 day-old healthy and uniformly grown rice seedlings were inoculated with diverse highly virulent  isolate of M. oryzae, Mo-ei-11. Conidia of M. oryzae isolates were collected from the culture grown on oatmeal agar plates by washing with 0.25% gelatin, with conidial concentration adjusted to 105 spores ml−1 using a haemocytometer. Inoculum was sprayed with an atomizer to create fine droplets of spore suspension which are retained on the plants. For mock control, plants were inoculated with 0.25% gelatin only.

tag: tissue

value: Leaf

tag: genotype

tag: age

value: 14 day old seedling


title: B_Lymph_A10

value: CCGTTAAG

tag: umi coordinate

tag: barcode coordinate

tag: apc ter119

tag: cd3 al700


title: mock inoculated leaf at 48 hpi, mo-ei-11 expt, biological replicate 3

description: gene expression data from mock inoculated rice leaf tissues at 48 hours post inoculation (hpi), Mo-ei-11 experiment


title: leaf at 48 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 3

description: gene expression data from rice leaf tissues at 48 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11

source_name: Rice leaf tissues at 48 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11


title: leaf at 72 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 3

description: gene expression data from rice leaf tissues at 72 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11

source_name: Rice leaf tissues at 72 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11


title: mock inoculated leaf at 48 hpi, mo-ei-11 expt, biological replicate 2

source_name: mock inoculated rice leaf tissues at 48 hours post inoculation (hpi), Mo-ei-11 experiment


title: leaf at 72 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 2


title: mock inoculated leaf at 72 hpi, mo-ei-11 expt, biological replicate 3

source_name: mock inoculated rice leaf tissues at 72 hours post inoculation (hpi), Mo-ei-11 experiment


title: leaf at 72 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 1


title: leaf at 48 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 1


title: mock inoculated leaf at 72 hpi, mo-ei-11 expt, biological replicate 2


title: leaf at 24 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 3

description: gene expression data from rice leaf tissues at 24 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11

source_name: Rice leaf tissues at 24 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11


title: mock inoculated leaf at 48 hpi, mo-ei-11 expt, biological replicate 1


title: B_Lymph_A7

value: TCCAGTAG

tag: fsc-a

tag: gr1 pe

tag: pe-cy7 sca-1

tag: mac-1 ef450


title: leaf at 48 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 2


title: leaf at 24 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 1


title: mock inoculated leaf at 24 hpi, mo-ei-11 expt, biological replicate 2

description: gene expression data from mock inoculated rice leaf tissues at 24 hours post inoculation (hpi), Mo-ei-11 experiment


title: mock inoculated leaf at 24 hpi, mo-ei-11 expt, biological replicate 3

source_name: mock inoculated rice leaf tissues at 24 hours post inoculation (hpi), Mo-ei-11 experiment


title: leaf at 24 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 2


title: mock inoculated leaf at 12 hpi, mo-ei-11 expt, biological replicate 2

description: gene expression data from mock inoculated rice leaf tissues at 12 hours post inoculation (hpi), Mo-ei-11 experiment


title: mock inoculated leaf at 24 hpi, mo-ei-11 expt, biological replicate 1


title: mock inoculated leaf at 12 hpi, mo-ei-11 expt, biological replicate 3

source_name: mock inoculated rice leaf tissues at 12 hours post inoculation (hpi), Mo-ei-11 experiment


title: leaf at 12 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 3

description: gene expression data from rice leaf tissues at 12 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11

source_name: Rice leaf tissues at 12 hours post inoculation (hpi) with M. oryzae isolate Mo-ei-11


title: leaf at 12 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 2


title: mock inoculated leaf at 12 hpi, mo-ei-11 expt, biological replicate 1


title: leaf at 12 hpi with M. oryzae isolate Mo-ei-11 , biological replicate 1


title: B_Lymph_A6

value: GACTGTAC

tag: fsc-h

tag: ssc-a

tag: time

tag: b220 apc cy7


title: B_Lymph_A5

tag: cell type

value: TAGTGCGT

tag: fitc cd44

tag: pcp cy55 c-kit

tag: fg


title: B_Lymph_A4

tag: barcode sequence

value: GTCCGAAT


title: B_Lymph_A9

value: GATGCGTT

tag: umi coordinate

value: 1 to 6 in R1


title: B_Lymph_A8

value: AGCGTTGT

tag: barcode coordinate


title: B_Lymph_A3

value: GGTCTATG

value: 7 to 14 in R1

tag: apc ter119


title: HL-1_siAirn_IgG.3

description: siAirn-001.1-transfected, anti-IgG RIP, biological rep3

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de).

source_name: HL-1 cells

growth_protocol: HL-1 cells are gift from Prof. Dr. William C. Claycomb (Louisiana State University Health Sciences Center). The cells were cultured according to the protocol by Dr. Claycomb using Claycomb Medium (Sigma-Aldrich, #51800C) supplemented with 10% fetal bovine serum (Sigma-Aldrich, #F2442; batch approved by Dr. Claycomb), 2mM L-glutamine (Sigma-Aldrich, #G7513), 0.1mM Norepienphrine (Sigma-Aldrich, #A0937), and antibiotics.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instruction.

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. RIP assay was performed using Magna RIP Kit (Millipore) following manufacturer's protocol.


title: HL-1_siAirn_Igf2bp2.4

description: siAirn-001.1-transfected, anti-Igf2bp2 RIP, biological rep4


title: HL-1_siScr_Igf2bp2.4

description: siScramble-transfected, anti-Igf2bp2 RIP, biological rep4


title: HL-1_siAirn_Igf2bp2.3

description: siAirn-001.1-transfected, anti-Igf2bp2 RIP, biological rep3


title: HL-1_siScr_IgG.3

description: siScramble-transfected, anti-IgG RIP, biological rep3


title: HL-1_siScr_Igf2bp2.3

description: siScramble-transfected, anti-Igf2bp2 RIP, biological rep3


title: P5-OC-Tg/Tg, biological rep5

city: Omaha

first: Michael

middle: D

last: Weston

state: Nebraska

address: 780729 California Plaza

department: Oral Biology

institute: Creighton University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: 2-way (Genotype, Age) ANOVA block design using the Linear Model for Microarray Data (Limma) Package through implementation of MicroArray Я US Gui interface to R and the Bioconductor Project microarray analysis programs.

source_name: OC, Tg/Tg

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen RNAeasy Mini Kit Total RNA extraction was performed according to the manufacturer's instructions.

tag: tissue

value: Cochlea

tag: genotype

value: Tg/Tg

tag: age

value: PostNatal day 18.5


title: P5-OC-WT, biological rep2

source_name: OC, WT


title: HL-1_siAirn_IgG.4

city: Copenhagen SV

first: Shizuka

last: Uchida

address: Frederikskaj 10B, 2. (building C)

institute: Aalborg University

description: siAirn-001.1-transfected, anti-IgG RIP, biological rep4


title: HL-1_siScr_IgG.4

description: siScramble-transfected, anti-IgG RIP, biological rep4


title: P5-OC-WT, biological rep1


title: P5-OC-WT, biological rep3

value: WT


title: P5-OC-WT, biological rep4


title: P5-OC-Tg/Tg, biological rep2

value: Organ of Corti

value: PostNatal day 5.5


title: P5-OC-Tg/Tg, biological rep4


title: P18-Cochlea-Tg/Tg, biological rep3

source_name: Cochlea, Tg/Tg


title: P18-Cochlea-WT, biological rep1

source_name: Cochea, WT


title: P5-OC-WT, biological rep5


title: Prelim Rd5

source_name: A549-GeCKO_Prelim Rd5

tag: cell line background

value: Human lung epithelial cells

tag: genotype/variation

value: A549-GeCKO; pooled library of A549 cells lacking individual gene

tag: subjected to

value: 5 consecutive rounds of lethal influenza virus infection (H5N1 low pathogenic)


title: P5-OC-Tg/Tg, biological rep1


title: A549-GeCKO library

source_name: A549-GeCKO library

tag: tranduced with

value: sgRNA lentivirus library (parental library)


title: P5-OC-Tg/Tg, biological rep3


title: P18-Cochlea-WT, biological rep2


title: P18-Cochlea-WT, biological rep3


title: P18-Cochlea-Tg/Tg, biological rep2


title: kidney 3 week control rep3

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne

description: gene expression data

hyb_protocol: Affymetrix mouse gene 1.0ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: RMA algorithm was applied to data, using Affymetrix Expression Console software.

source_name: mouse whole kidney

label_protocol: For each sample, 100ng of total RNA were amplified using the Ambion® WT Expression Kit (4411973, life technologies) kit. 5.5μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

growth_protocol: mice were housed in standard 12h Light/12h dark light regimen

extract_protocol: Trizol extraction of total RNA, followed by purification with the RNeasy Mini Kit (Qiagen).

treatment_protocol: at the indicated age mice were sacrificed with CO2 and whole kidney was collected for RNA extraction

tag: strain

value: Mixed C57BL6/SV129

value: 3 weeks


title: kidney 3 week FVB control rep2

description: gene expression data

value: FVB


title: kidney 3 week AZIP rep3

description: gene expression data


title: kidney 3 week FVB control rep3

description: gene expression data


title: kidney 3 week AZIP rep1

description: gene expression data


title: kidney 3 week PpargΔ/Δ rep2

description: gene expression data


title: kidney 3 week AZIP rep2

description: gene expression data


title: kidney 3 week PpargΔ/Δ rep1

description: gene expression data


title: kidney 3 week control rep1

description: gene expression data


title: kidney 3 week FVB control rep1

description: gene expression data


title: kidney 3 week control rep2

description: gene expression data


title: Female ALN sample 16, rep5

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the Asurgen Services facility in Austin TX, USA

data_processing: Raw array data (CEL files) were loaded into the R statistical environment (v3.2.5) using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. An updated Probe to Entrez Gene ID map, hugene20sthsentrezgcdf (v20.0.0), was used for annotation.

source_name: Peripheral blood, female, ALN

extract_protocol: Total RNA was isolated from blood archived in PAXgene tubes utilizing the PAXgene Blood RNA Kit (Qiagen, Basel, Switzerland) with modifications to improve RNA yield and quality

tag: disease state

value: SLE

tag: nephritis state

value: active LN (ALN)

tag: Sex

value: female

tag: disease duration

tag: sledai

tag: steroid treatment

tag: antimalarial treatment

tag: immunosuppressive treatment

tag: biopsy class

value: IV

tag: chronicity

tag: activity

value: Peripheral blood


title: kidney 3 week PpargΔ/Δ rep3

description: gene expression data

tag: age


title: Normal esophageal tissue_Riboflavin deficiency combined with NMBA (R0N+)_rep2

city: Shantou

first: Feng

last: Pan

address: No.22, Xinling Road

institute: Medical College of Shantou University

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix)in a Hybridization Oven 645 ( Affymetrix)and a Fluidics Station 450 (Affymetrix) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip Scanner 3000 (Affymetrix).

data_processing:
Command Console Software (Affymetrix) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.
RMA expression value derived from Expression Console software (Affymetrix).

organism: Rattus norvegicus

label_protocol: Total RNA was amplified, labeled and purified by Ovation FFPE WTA System (NuGEN) and FL-Ovation™ cDNA Biotin Module V2(NuGEN) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Total RNA was extracted and purified using Total Nucleic Acid Isolation Kit for FFPE (Life Technologies) following the manufacturer’ s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies).

treatment_protocol: All rats received subcutaneous injection NMBA (0.35 mg/kg ) three times per week for 5 weeks. At the same time, rats were fed the diet with either riboflavin-deficient or normal riboflavin diets for the duration of the experiment. All rats were euthanized at week 25. Esophageal tissues were paraformaldehyde fixed, paraffin-embedded. The tissue of interest was isolated and placed in an microcentrifuge tube.

tag: diet

value: Riboflavin deficiency

tag: tissue

value: Esophagus - normal


title: Female ALN sample 16, rep4

scan_protocol: Manufacturer's recommended protocols as followed by the Asurgen Services facility in Austin TX, USA


title: Esophageal epithelial neoplasia_Riboflavin normal combined with NMBA (RcN+)_rep2

value: Riboflavin normal

value: Esophagus - Esophageal epithelial neoplasia


title: P18-Cochlea-Tg/Tg, biological rep1

value: Organ of Corti

tag: genotype

value: Tg/Tg

value: PostNatal day 5.5


title: Female ALN sample 16, rep3

label_protocol: Manufacturer's recommended protocols as followed by the Asurgen Services facility in Austin TX, USA


title: Esophageal epithelial neoplasia_Riboflavin deficiency combined with NMBA (R0N+)_rep2


title: Normal esophageal tissue_Riboflavin deficiency combined with NMBA (R0N+)_rep1


title: Normal esophageal tissue_Riboflavin normal combined with NMBA (RcN+)_rep2


title: Normal esophageal tissue_Riboflavin normal combined with NMBA (RcN+)_rep1


title: Esophageal epithelial neoplasia_Riboflavin deficiency combined with NMBA (R0N+)_rep1


title: Esophageal epithelial neoplasia_Riboflavin normal combined with NMBA (RcN+)_rep1


title: DMSO treated replicate 3

city: Durham

first: Khadar

last: Abdi

state: NC

address: 300 North Duke St.

department: DMPI

institute: Duke University

hyb_protocol: Hybridization of targets were prepared from total RNA using a MessagAmp Premier RNA Amplificaiton Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 7G according to the standard Affymetrix GeneChip manufacturer instructions.

data_processing: Affymetrix Gene Chip microarray data underwent strict quality control processing using the simpleaffy package in the Bioconductor2 suite from the R statistical programming environment. Log-scale Robust Multiarray Analysis (RMA) from the  affy package was used to normalize the data and eliminate systematic differences across the arrays. Differential expression of genes across the conditions was identified from a moderated test statistic employed by the limma package. The False Discovery Rate (FDR) method was used to correct for multiple hypothesis testing.

source_name: ependymal culture DMSO treated

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Total RNA was labeled and hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: Ependymal cultures were differentiated from radial glial progenitors and grown in differentiation media contain DMEM/F12, 2% FBS, penstrep.

extract_protocol: Total RNA was extracted from ependymal cultures using RNA easy minikit (Invitrogen) and cDNA was prepared using Superscript Vilo cDNA synthesis kit (Invitrogen).

treatment_protocol: Fully differentiated ependymal cell cultures (2 weeks) were either treated with DMSO as a control or with 0.25 uM MLN4924 for 36 hours.

tag: cell type

value: primary ependymal culture

tag: treatment

value: DMSO treated cultures


title: MLN4924 treated replicate 1

source_name: ependymal culture MLN4924 treated

value: MLN4924 treated cultures


title: MLN4924 treated replicate 3


title: Female ALN sample 16, rep2

tag: disease state


title: Female control sample 13

source_name: Peripheral blood, female, control

value: control


title: Female control sample 12


title: Female control sample 14


title: Female control sample 10


title: Female control sample 8


title: Female control sample 11


title: MLN4924 treated replicate 2


title: WT without ATc rep 2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

description:
rRNA-depeleted
WT_no_Atc_2_NO-65
RNA-seq_mihF_CountTable.txt
DESeq2_RvAtc_vs_RvNoAtc_v2.csv

data_processing:
Basecalling was done with the Illumina Pipeline Software version 1.84.
Reads were adapter- and quality-trimmed with Trimmomatic v0.33. The quality settings were “SLIDINGWINDOW:5:15 MINLEN:40”
Reads were aligned with Bowtie2 against the H37Rv reference sequence (NC_000962.3).
Counting reads over annotated features was done with featureCounts. Annotation was taken from TubercuList release R27 (http://tuberculist.epfl.ch/).
Differential gene expression analysis was done using DESeq2
Genome_build: NC_000962.3
Supplementary_files_format_and_content: .txt file includes counts.
.csv files include differential gene expressin results obrained with DESeq2, between treated and untreated conditions

organism: Mycobacterium tuberculosis

source_name: bacterial culture

growth_protocol: M. tuberculosis H37Rv and mihF-cKD strains were grown at 37°C either in Middlebrook 7H9 broth (Difco) supplemented with 10% albumin-dextrose-catalase, 0.2 % glycerol and 0.05% Tween 80 or in Sauton’s liquid medium supplemented with 0.005% Tween 80. Cultures were plated on Middlebrook 7H10 (Difco) agar supplemented with 10% oleic acid-albumin-dextrose-catalase and 0.2% glycerol.

extract_protocol:
M. tuberculosis H37Rv and mihF-cKD cultures were harvested by centrifugation, pellets were resuspended in TRIzol Reagent (ThermoFisher) and stored at -80°C until further processing. Total RNA was extracted by bead-beating as previously described (Jungwirth et al., 2012). Integrity of RNA was checked by agarose gel electrophoresis, purity and amount of RNA were assessed using a Nanodrop instrument and Qubit Fluorometric Quantitation (ThermoFisher) respectively. SuperScript III First-Strand Synthesis System (Invitrogen) was used to generate randomly primed cDNA from 500 ng of RNA, according to the manufacturer’s recommendations. The ribosomal RNA was depleted with the Ribo-Zero rRNA Removal Kit for Gram-positive Bacteria (Illumina), following the manufacturer’s instructions.
Libraries were prepared using the Truseq Stranded mRNA Library Prep kit reagents (Illumina) according to the manufacturer’s recommendations. The multiplexed libraries were sequenced on a Hiseq 2500 instrument using TruSeq SBS Kit V4 reagents as single-end 100 nt-long reads.

treatment_protocol: Anhydrotetracycline (ATc, Clontech, 600 ng ml−1) was added to the growth medium.

tag: strain

value: WT

tag: growth medium

value: without ATc


title: Female control sample 9

tag: Sex

tag: disease duration


title: Male control sample 3

source_name: Peripheral blood, male, control

value: male

tag: sledai

tag: steroid treatment


title: Male control sample 1

tag: antimalarial treatment

tag: immunosuppressive treatment


title: Female control sample 4

value: female

tag: biopsy class

tag: chronicity


title: DMSO treated replicate 2


title: DMSO treated replicate 1


title: Female control sample 3

tag: age

tag: activity


title: Female control sample 6

tag: tissue


title: Female control sample 2


title: Male ALN sample 7

source_name: Peripheral blood, male, ALN

value: SLE

tag: nephritis state

value: active LN (ALN)

value: IV, V


title: Female ALN sample 18

value: IV

value: Peripheral blood


title: Female control sample 7


title: Female ALN sample 17


title: Female ALN sample 13


title: Male ALN sample 6

value: III


title: WT with ATc rep 2

description:
rRNA-depeleted
WT_Atc_2_NO-67
RNA-seq_mihF_CountTable.txt
DESeq2_RvAtc_vs_RvNoAtc_v2.csv

tag: genotype

value: with ATc


title: Female control sample 1


title: Female ALN sample 15


title: Female ALN sample 16, rep1


title: Female control sample 5


title: Female ALN sample 12


title: mihF mutant with ATc rep 2

description:
rRNA-depeleted
mihF_cKD_Atc_2_NO-2
RNA-seq_mihF_CountTable.txt
DESeq2_MutAtc_vs_MutNoAtc_v2.csv

value: mIHF-cKD


title: WT without ATc rep 1

description:
rRNA-depeleted
WT_no_Atc_1_NO-64
RNA-seq_mihF_CountTable.txt
DESeq2_RvAtc_vs_RvNoAtc_v2.csv


title: Female ALN sample 11

value: V


title: mihF mutant without ATc rep 2

description:
rRNA-depeleted
mihF_cKD_no_Atc_2_NO-69
RNA-seq_mihF_CountTable.txt
DESeq2_MutAtc_vs_MutNoAtc_v2.csv


title: espR ChIPseq

description: EspR

data_processing:
Alignment was performed with Bowtie2
HOMER was used for peak calling, using the dynamic peak size algorithm and the input as a control.
Peaks were annotated and further analyzed with BEDtools and deepTools
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Tab-delimited file including peak predictions.

growth_protocol: M. tuberculosis cultures were grown in 7H9 medium.

extract_protocol:
Exponentially growing M. tuberculosis H37Rv liquid cultures were cross-linked with formalin 1 % for 10’ and quenched with glycine 125 mM for 10’, washed twice in Tris-buffered saline (TBS, pH 7.5) and sonicated on a Diagenode Bioruptor with 30’’ on/off cycles for 10’ on high settings to shear DNA to 200 – 500 bp fragments. Immunoprecipitation was performed with monoclonal anti-mIHF (Alere) or polyclonal rat anti-EspR antibodies (Statens Serum Institut, Copenhagen, Denmark) in 1 ml immunoprecipitation (IP) buffer (containing 50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM ethylendiaminetetraacetic acid (EDTA), 1 % Triton X-100, 0.1 % (w/v) sodium deoxycholate, 0.1 % sodium dodecyl sulphate (SDS) and one protease inhibitor cocktail tablet (Roche)) overnight at 4°C. 100 µl Dynabeads sheep anti-rag IgG (Dynal Biotech) for EspR and 100 µl per sample anti-ProteinL magnetic beads (Pierce) for mIHF were pre-saturated with 1mg ml-1 bovine serum albumin and 0.1 mg ml-1 salmon sperm DNA, then incubated with each corresponding sample for four hours. The IP was washed 5 times with increasing stringency buffers.
Libraries were prepared with the NEBNext Ultra II DNA kit (NEB) following the manufacturer’s instructions

value: wild type

tag: chip antibody


title: mIHF ChIPseq

value: monoclonal anti-mIHF antibodies (Alere)


title: Female ALN sample 14

tag: disease state


title: Female ALN sample 9

value: III, V


title: mihF mutant with ATc rep 1

description:
rRNA-depeleted
mihF_cKD_Atc_1_NO-1
RNA-seq_mihF_CountTable.txt
DESeq2_MutAtc_vs_MutNoAtc_v2.csv

tag: strain


title: Male ALN sample 4


title: input DNA

description: Inp


title: mIHF-depleted cKD mutant ChIPseq


title: Male ALN sample 5


title: Female ALN sample 10


title: Female ANLN sample 12

source_name: Peripheral blood, female, ANLN

value: without LN (ANLN)


title: Female ANLN sample 10


title: Female ALN sample 8


title: Female ALN sample 7


title: WT with ATc rep 1

description:
rRNA-depeleted
WT_Atc_1_NO-66
RNA-seq_mihF_CountTable.txt
DESeq2_RvAtc_vs_RvNoAtc_v2.csv

value: WT

tag: growth medium


title: Female ANLN sample 7

tag: Sex


title: Female ALN sample 6

tag: disease duration


title: Male ANLN sample 1

source_name: Peripheral blood, male, ANLN

tag: sledai


title: Female ANLN sample 8

tag: steroid treatment


title: Female ANLN sample 6

tag: antimalarial treatment


title: Male control sample 2

value: control

tag: immunosuppressive treatment


title: Female ANLN sample 5

tag: biopsy class


title: Female ANLN sample 11

tag: chronicity


title: Female ANLN sample 9

tag: age


title: Female ANLN sample 4

tag: activity


title: Female ALN sample 5

tag: tissue


title: primary fibroblast, d1; rep1

city: Braunschweig

first: Tobias

last: May

address: Inhoffenstrasse 7

institute: InSCREENeX GmbH

description: primary fibroblast, donor1; replicate 1

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip HG-U133 Plus 2.0 for 16 hours at 45°C. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the recommended FS450 protocol (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Data were analyzed using GeneSpring 11.5.1 (Agilent Technologies, CA, USA) software applying RMA probe summarization algorithm.

source_name: primary human gingiva fibroblasts

label_protocol: 500 ng of total RNA were used for biotin labelling according the 3´ IVT Express Kit (Affymetrix; Santa Clara, CA). 7.5 µg of biotinylated cRNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer.

extract_protocol: Extraction of total RNA was done using RNeasy Mini Kit (Qiagen) in combination with QIAschredder (Qiagen) according to the manufacturer's instructions.

tag: cell type

value: primary fibroblast

tag: cell source

value: primary human gingiva fibroblasts, donor 1


title: Day4 microglia bio replicate 7

city: iowa City

first: Dorthea

last: Wheeler

state: IA

address: 51 Newton Road

institute: University of Iowa

hyb_protocol: Following fragmentation, ds-cDNA were hybridized for 18 hr at 45C  with 60 rpm rotation on Affymatrix mouse Clariom S array.

scan_protocol: Clariom S array was scanned using Affymatrix Model 3000 scanner.

data_processing:
Partek Genomics Suite was used to analyze the data. RMA analysis was used. Anova-generated p-values were corrected using false-discovery rate. Genes with adjusted p-values <0.05 and a fold-change >2 was considered significant.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: microglia from day 4 post-infection 6-week old mouse brains

label_protocol: Biotinylated ds -cDNA were prepared according to the standard Affymetrix protocol from 1 ng total RNA (3' IVT Pico Reagent Kit, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

value: 6 weeks

tag: infection status

value: day 4 post-MHV infection

tag: time point

value: day 4 post-MHV-infection

value: brain

value: FACS-sorted microglia


title: primary fibroblast, d2

description: primary fibroblast, donor2

value: primary human gingiva fibroblasts, donor 2


title: Day4 microglia bio replicate 8

tag: strain


title: Day4 microglia bio replicate 6


title: primary fibroblast, d3

description: primary fibroblast, donor3

value: primary human gingiva fibroblasts, donor 3


title: Day4 microglia bio replicate 1


title: primary fibroblast, d1; rep2

description: primary fibroblast, donor1; replicate 2


title: e-hUVEC-2; rep1

description: immortalized HUVEC line e-hUVEC-9; replicate 1

source_name: immortalized human endothelial cell line e-hUVEC-2

value: immortalized HUVEC

value: immortalized human endothelial cells from the umbilical cord


title: e-hUVEC-2; rep2

description: immortalized HUVEC line e-hUVEC-9; replicate 2


title: Female ANLN sample 3

tag: disease state

value: SLE

tag: nephritis state

tag: Sex

value: female

value: Peripheral blood


title: Female ALN sample 4

value: active LN (ALN)

tag: disease duration

tag: sledai

tag: steroid treatment

value: IV


title: e-hUVEC-8; rep1

description: immortalized HUVEC line e-hUVEC-8; replicate 1

source_name: immortalized human endothelial cell line e-hUVEC-8


title: Naïve Microglia bio replicate 3

source_name: microglia from naïve 6-week old mice

value: naïve


title: Naïve Microglia bio replicate 2


title: e-hUVEC-8; rep2

description: immortalized HUVEC line e-hUVEC-8; replicate 2


title: Naïve Microglia bio replicate 4


title: Female ALN sample 1

tag: antimalarial treatment

tag: immunosuppressive treatment

tag: biopsy class

value: V