title: MF303_CTCL_scRNA_Patient_PBMCs

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (refdata-cellranger-GRCh38-3.0.0)  and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Reads from TCR receptor libraries were assembled using the 'cellranger vdj' pipeline in the reference-assisted mode using the vdj_GRCh38_alts_ensembl-3.1.0.reference version
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: PBMCs

extract_protocol:
A 6mm skin punch biopsy from an MF lesion was obtained from the right flank. The biopsy was minced with scalpels and digested in collagenase IV (0,5U/ml, Worthington) for 30min at 37°C to obtain a single cell suspension. Lymph node cells were obtained from a small fraction of a diagnostic biopsy from a pathologically enlarged axillary lymph node. PBMC were prepared by Ficoll® Paque density gradient centrifugation (GE Healthcare). All cell suspensions were frozen at -80°C until further processing. Cell suspensions were thawed and stained with CD7 FITC, CD4 PE, CD3 APC, CD45 ECD and 7-AAD. In the case of skin and lymph node, viable CD45+CD3+CD4+ T-helper cells, other CD45+ cells, and CD45-negative cells were sorted on a FACS Aria III (BD Biosciences) at a ratio of 1:2:1. In the case of PBMC, viable CD3+CD4+ helper T-cells and remaining CD45+ cells were sorted in a ratio of 1:2. Immediately after sorting, cells were subjected to scRNA-seq processing (10X Genomics, Pleasanton, CA) according to the manufacturer’s instructions.
T-cell-receptor (TCR) sequencing and 5’ gene expression sequencing was performed using the Chromium Controller and Single Cell 5’ Library & Gel Bead Kit and the V(D)J Kit (10x Genomics), respectively, according to the manufacturer’s protocol. Sequencing was performed using the Illumina HiSeq 4000 platform and the 150bp paired-end configuration.

tag: diagnosis

value: Mycosis fungoides

tag: location

value: blood

value: PBMCs

tag: chemistry

value: Single Cell 5' PE/ Single Cell V(D)J


title: Paracoccus denitrificans ATCC19367-control-3

status: Public on Apr 13 2021

type: SRA

city: Guangzhou

first: Mei

last: Wang

state: Guangdong

address: 483 Wushan Road

department: College of Veterinary Medicine

country: China

institute: South China Agricultural University

library_source: transcriptomic

data_processing:
Bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Paracoccus denitrificans ASM406373v1 whole genome using bowtie2 (v2.2.6).
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi and Williams, Nature methods, 2008.
Genome_build: Paracoccus denitrificans ASM406373v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Paracoccus denitrificans

extract_protocol:
Paracoccus denitrificans was collected by centrifugation, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard IIIuminia protocols

tag: agent

tag: strain


title: BG-H3K9me3-ChIP-WT-1

city: Xiamen

first: shaoxuan

last: chen

state: Fujian Province

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: xiamen university

library_source: genomic

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
clean reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.2.8).
Enriched peaks of H3K9me3 were identified by HOMER v4.10.1 with histone style (http://homer.ucsd.edu/homer).
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: cerebellum

extract_protocol:
Approximately 5 x 10^6 Bergmann glial cells isolated as above was fixed in 1% formaldehyde for 10 min at room temperature (RT), followed by quenching in 125 nM glycine for 5 min. Cell nuclei were collected and lysed in lysing buffer (50 mM HEPES/KOH pH 7.6, 1 mM EDTA, 140 nM NaCl, 10 % v/v Glycerol, 0.5 % NP-40, 0.25 % v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with 1.5μg H3K9me3 antibody (rabbit, Abcam, #ab232324) overnight at 4 °C, followed with collection using 30 μL protein A/G plus agarose beads (Millipore).
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

tag: tissue

value: Bergmann glia

tag: antibody

tag: age

value: post natal day 10


title: ABEmax_3mg/kg_redose_Primary_Hepatocytes_Rep3

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

source_name: primary hepatocytes

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: LNP-mediated delivery

value: tail vein

value: targeted amplicon sequencing

tag: genotype

value: base-edited PCSK9


title: Mouse epiblast stem cells - Blastocyst-like Hemisphere Reprogramming Day 5 population

city: Kobe

first: Cody

last: Kime

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
BAM files were produced with Cell Ranger (Version 3.1)
Counts were split to intron and exon counts with dropEst
Basic cell quality filtering was performed in Seurat
SkewC was performed after Seurat to remove skewed and retain typical cells, producing a final total high quality filtering of cell samples to the filteredcellbarcodes list.
Final exon, intron, and sum (exon+intron) count tables from DropEst are generated from filtered barcodes set for downstream use as R Data files (*modifiedCCM.rds).
Genome_build: Mus musculus mm10 reference genome with EGFP and mCherry transgenes in custom GTF, included as genes.gtf.
Supplementary_files_format_and_content: List of post-filtered cell barcodes used in the study, prepared as a tsv file.
Supplementary_files_format_and_content: *modifiedCCM.rds with processed count tables and barcodes for each sample.

molecule: polyA RNA

source_name: XGFP and MERVL::mCherry reporter mouse epiblast stem cells undergoing reprogramming

extract_protocol:
Cells were digested to single cell with accutase for 10-15 minutes, screened, and resuspended in low FBS Phosphate Buffered Saline solution, counted 16 times for cell concentration, viability, and doublet rate, and then diluted to approprate loading concentrations for the 10X Genomics Chromium Controller.
scRNA-seq libraries were prepared with 10x Genomics Chromium system using 3' (V3.0 chemistry) GEM beads and i7 Index kit following standard protocol. Libraries were diluted and submitted to Macrogen for sequencing under the library strategy.
Libraries were sequenced using paired-end sequencing (150bp Read 1 and 150bp Read 2) with a single sample per lane on the Illumina HiSeq X

tag: strain/genotype

value: Tg(CAG-EGFP)D4Nagy; 129X1/SvJ x 129S1/Sv)F1-Kitl; Piggybac MERVL::mCherry

tag: culture protocol

tag: culture plate

value: Fibronectin coated plate


title: ABEmax_3mg/kg_Liver_Rep1

source_name: whole liver lysate


title: ABEmax_1mg/kg_Liver_Rep1


title: MF303_CTCL_scRNA_Patient_LN ·

organism: Homo sapiens

source_name: lymph node biopsy

value: axillary lymph node

value: lymph node biopsy


title: ABEmax_3mg/kg_redose_Liver_Rep3


title: Paracoccus denitrificans ATCC19367-control-2


title: MF303_CTCL_scRNA_Patient_Skin

source_name: skin biopsy

value: right flank

value: skin biopsy


title: BG-input-2

value: IgG


title: Paracoccus denitrificans ATCC19367-control-1


title: 09_K562_LUC7L2_KO_Glu

city: Cambridge

first: Alexis

middle: A

last: Jourdain

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute of MIT & Harvard

data_processing:
The reads were aligned with STAR (Dobin et al., 2013) to the human genome hg19 using default parameters and a two-pass approach.
Following a first pass alignment of each sample, novel splice junctions were pooled across all samples from the same cell type and incorporated into the genome annotation for a second pass alignment.
Second pass gene counts derived from uniquely mapping pairs with the expected strandedness were output by STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: K562 cells

growth_protocol: LUC7L2 WT and LUC7L2 KO HeLa and K562 cells were were maintained in DMEM containing 1mM sodium pyruvate (ThermoFisher Scientific) with 25 mM glucose, 10% fetal bovine serum (FBS, ThermoFisher Scientific), 50 μg/mL uridine (Sigma), and 100 U/mL penicillin/streptomycin (ThermoFisher Scientific) under 5% CO2 at 37°C.

extract_protocol:
Total RNA from LUC7L2 WT and LUC7L2 KO K562 and HeLa cells (N=3, each) were isolated using a RNeasy kit (QIAGEN).
RNA sequencing libraries were prepared by the Genomics Platform at the Broad Institute based on the True-Seq protocol (Illumina), which selects for polyadenylated RNA and preserves strand specificity. Libraries were sequenced using a NovaSeq 6000 instrument, generating 2x101bp paired-end reads with a minimum of 40M pairs per sample.

treatment_protocol: For galactose growth, FBS was replaced by dialyzed FBS (Life Technologies) and glucose was replaced by an equivalent amount of galactose.

tag: cell type

value: K562 cells

value: LUC7L2 KO

tag: culture condition

value: DMEM with 25mM glucose


title: BG-input-1


title: ABEmax_3mg/kg_redose_Primary_Hepatocytes_Rep2


title: 08_K562_LUC7L2_KO_Glu


title: ABEmax_3mg/kg_redose_Liver_Rep2


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep1


title: Paracoccus denitrificans ATCC19367-florfenicol-treated-1

value: florfenicol


title: 07_K562_LUC7L2_KO_Glu


title: 06_K562_LUC7L2_WT_GAL

value: LUC7L2 WT

value: DMEM with 25mM galactose


title: ABEmax_3mg/kg_redose_Primary_Hepatocytes_Rep1

value: LNP-mediated delivery


title: 05_K562_LUC7L2_WT_GAL


title: ABEmax_3mg/kg_redose_Liver_Rep1

value: tail vein


title: 04_K562_LUC7L2_WT_GAL


title: ABEmax-dCas_Primary_Hepatocytes_Rep2

value: AAV-mediated delivery

value: targeted amplicon sequencing


title: C. tropicalis CEM010 Biofilm Growth in RPMI Replicate 2

type: RNA

city: Irapuato

first: Eugenio

last: Mancera

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Ingenieria Genetica

country: Mexico

institute: Cinvestav

hyb_protocol: Equal amounts of the Cy3 and Cy5 labeled cDNA hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.

scan_protocol: Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed first by averaging the result for all duplicate probes and finally by taking the median of the probes for each ORF. Data was transformed as described for each experiment. Note that comparisons between arrays can only be made if they share a pooled reference (Ch2)

organism: Candida tropicalis

source_name: CEM010 RPMI biofilm

label_protocol: cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).

growth_protocol: Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.

extract_protocol: RNA was isolated and reverse transcribed as previously described (Nobile et al. 2012). Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.

treatment_protocol: Nobile et al. Cell 2012

tag: media

value: RPMI

tag: growth

value: biofilm

source_name: pooled reference

tag: sample type

value: pooled reference


title: C. tropicalis CEM010 Biofilm Growth in RPMI Replicate 1


title: C. tropicalis CEM010 Biofilm Growth in Spider Glucose Replicate 2

source_name: CEM010 spider glucose biofilm

value: Spider glucose


title: Irradiation 3Gy 24h, biological rep 3 [miRNA]

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: 04 3 Gy 24h_3

hyb_protocol: Biotin-labeled miRNA were hybridized to Applied Biosystems™ miRNA 4.1 Array Strip (20 h, 48 °C). Then, the microarrays were subjected to a washing and staining procedure, according to the technical protocol, using the Affymetrix GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: hiPSCs_Irradiation 3Gy 24h

label_protocol: The complete procedure for preparing miRNA for hybridization was performed using the FlashTagTM Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, Waltham, MA, USA). 150 ng of previously isolated miRNA was subjected to poly(A) tailing and biotin ligation procedure, according to producer protocol.

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were used to form EBs. After 7 days, the EBs were differentiated into a chondrogenic lineage in a defined medium supplemented with TGF-β (10 ng/ml).

extract_protocol: Total RNA with miRNA was purified with TRI Reagent solution according to the manufacturer’s protocol.

treatment_protocol: Treatment plans were prepared using volumetric modulated arc therapy (VMAT) technique using 2 co-planar arcs. The goal of the plans was to cover at least 95% of the PTV with the planned prescription dose: 1, 2 and 3 Gy.

tag: treatment

value: Irradiation 3Gy 24h


title: Irradiation 3Gy 24h, biological rep 1 [miRNA]

description: 04 3 Gy 24h

value: Human induced pluripotent stem cells (hiPSCs)


title: Irradiation 3Gy 24h, biological rep 2 [miRNA]

description: 04 3 Gy 24h_2


title: ABEmax-dCas_Liver_Rep2

value: base-edited PCSK9


title: Irradiation 2Gy 24h, biological rep 3 [miRNA]

description: 03 2 Gy 24h_3

source_name: hiPSCs_Irradiation 2Gy 24h

value: Irradiation 2Gy 24h


title: C. tropicalis CEM010 Planktonic Growth in RPMI Replicate 2

source_name: CEM010 RPMI planktonic

value: planktonic


title: Irradiation 2Gy 24h, biological rep 2 [miRNA]

description: 03 2 Gy 24h_2


title: C. tropicalis CEM010 Biofilm Growth in Spider Glucose Replicate 1


title: 04_K562_LUC7L2_WT_Glu_B

value: K562 cells

value: DMEM with 25mM glucose


title: ABEmax-dCas_Primary_Hepatocytes_Rep1


title: ABEmax-dCas_Liver_Rep1


title: 03_K562_LUC7L2_WT_Glu

value: LUC7L2 WT


title: Irradiation 2Gy 24h, biological rep 1 [miRNA]

description: 03 2 Gy 24h


title: C. tropicalis CEM010 Planktonic Growth in Spider Glucose Replicate 2

source_name: CEM010 spider glucose planktonic


title: 02_K562_LUC7L2_WT_Glu


title: 18_HeLa_LUC7L2_KO_Glu

source_name: HeLa cells

value: HeLa cells

value: LUC7L2 KO


title: ABEmax_Primary_Hepatocytes_Rep3

value: tail vein


title: C. tropicalis CEM010 Planktonic Growth in RPMI Replicate 1


title: Irradiation 1Gy 24h, biological rep 3 [miRNA]

description: 02 1 Gy 24h_3

source_name: hiPSCs_Irradiation 1Gy 24h

value: Irradiation 1Gy 24h


title: Cd_untagged_spglu-2

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz
Supplementary_files_format_and_content: enrich.txt files have the maximum fold enrichment between tagged and untagged control experiment for each upstream intergenic region in the genome.

organism: Candida dubliniensis

source_name: a/alpha cell

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider and Spider 1% glucose for C. albicans and C. dubliniensis, and in RPMI 1% glucose and Spider 1% for C. tropicalis, samples were harvested.  Biofilm growth was done at 37°C and 200 rpm.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cell disruption and immunoprecipitation were performed as previously described (Hernday et al., Methods Enzymol 470: 737-758, 2010) using a c-Myc tag monoclonal antibody (RRID: AB_2536303).
Performed using an NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina sequencing

tag: dna-binding gene

tag: epitope

value: untagged

value: Spider 1% glucose

tag: chip antibody

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: ABEmax_Liver_Rep3

value: AAV-mediated delivery

value: targeted amplicon sequencing


title: C. tropicalis CEM010 Planktonic Growth in Spider Glucose Replicate 1

value: Spider glucose

value: pooled reference


title: 17_HeLa_LUC7L2_KO_Glu


title: Cd_untagged_spglu-1

value: biofilm


title: Irradiation 1Gy 24h, biological rep 2 [miRNA]

description: 02 1 Gy 24h_2

value: Human induced pluripotent stem cells (hiPSCs)


title: ABEmax_Primary_Hepatocytes_Rep2

value: base-edited PCSK9


title: Cd_untagged_spider-2

value: Spider


title: Irradiation 1Gy 24h, biological rep 1 [miRNA]

description: 02 1 Gy 24h


title: 16_HeLa_LUC7L2_KO_Glu

value: DMEM with 25mM glucose


title: Cd_untagged_spider-1


title: 15_HeLa_LUC7L2_WT_GAL

value: LUC7L2 WT

value: DMEM with 25mM galactose


title: ABEmax_Liver_Rep2


title: ABEmax_Primary_Hepatocytes_Rep1


title: Cd_Ndt80_spglu-2

description:
ChIPspglu_II_CEM261
samples for processed file: ChIPspglu_II_CEM261 - ChIPspglu_II_CEM080
cdub_bothmedia.enrich.txt

value: c-myc


title: 14_HeLa_LUC7L2_WT_GAL

value: HeLa cells


title: ABEmax_Liver_Rep1

value: tail vein


title: 13_HeLa_LUC7L2_WT_GAL


title: Control 24h, biological rep 3 [miRNA]

description: 01 ctrl 24h_3

source_name: hiPSCs_Control 24h

value: Control 24h


title: Cd_Ndt80_spglu-1

description:
ChIPspglu_I_CEM261
samples for processed file: ChIPspglu_I_CEM261 - ChIPspglu_I_CEM080
cdub_bothmedia.enrich.txt

value: Spider 1% glucose


title: Control 24h, biological rep 2 [miRNA]

description: 01 ctrl 24h_2


title: 04_HeLa_LUC7L2_WT_Glu_B


title: ABE8e_Primary_Hepatocytes_Rep2

source_name: primary hepatocytes


title: HR51_6h_B

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl DM6.gtf none -d [TAG DIR] -count 3utr -condenseGenes -strand +
Genome_build: DM6
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 DsRed+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Library constracted using MARS-seq technique (Jaitin et al, Science 2014). Briefly mRNA was barcoded, converted  into cDNA and linearly amplified by T7 in vitro transcription.
3' MARseq Jaitin et al, 2014

tag: developmental stage

value: pupae (6h after puparium formation)

tag: strain

value: Brain

tag: selection markers

value: DsRed +

value: gamma neurons


title: HR51_6h_C

tag: tissue


title: Cd_Ndt80_spider-2

description:
ChIP_II_CEM261
samples for processed file: ChIP_II_CEM261 - ChIP_II_CEM080
cdub_bothmedia.enrich.txt

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: HR51_6h_A


title: Control 24h, biological rep 1 [miRNA]

description: 01 ctrl 24h


title: 12_HeLa_LUC7L2_WT_Glu

tag: genotype


title: Cd_Ndt80_spider-1

description:
ChIP_I_CEM261
samples for processed file: ChIP_I_CEM261 - ChIP_I_CEM080
cdub_bothmedia.enrich.txt

value: biofilm


title: ABE8e_Primary_Hepatocytes_Rep1

value: AAV-mediated delivery

value: targeted amplicon sequencing


title: HR51_24h_C

value: pupae (24h after puparium formation)


title: ABE8e_Liver_Rep2

source_name: whole liver lysate

value: base-edited PCSK9


title: HR51_24h_B


title: ABE8e_Liver_Rep1


title: Cd_untagged_hom-2

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Adjusted the number of reads in the different treatment-control dataset pairs using SAMtools view -s function prior to peak calling
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz; www.candidagenome.org/download/sequence/C_parapsilosis_CDC317/archive/C_parapsilosis_CDC317_version_s01-m03-r13_chromosomes.fasta.gz
Supplementary_files_format_and_content: peaks.txt files were generated for each experiment with tagged proteins using untagged strains as a control in MACS2.

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider 1% glucose at 37°C and 200 rpm

value: untagged


title: 10_HeLa_LUC7L2_WT_Glu

value: LUC7L2 WT

value: DMEM with 25mM glucose


title: Cd_untagged_hom-1


title: Ad-shKLF11_4

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

data_processing:
The quality control of the sequencing reads for each sample was assessed with FastQC (Babraham Bioinformatics).
The human reference cDNA sequences were downloaded from the Ensembl database (GRCh38 ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/).
The reference was indexed with Salmon v 0.14.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and TPM value for each sample

source_name: human aortic endothelial cells

growth_protocol: Human aortic endothelial cells (HAECs, CC-2535) were purchased from Lonza (Walkersville, MD). HAECs were cultured in endothelial cell growth media-2 (EGM-2, CC-3202, Lonza, Walkersville, MD) at 37°C, 5% CO2 in a humidified cell culture incubator.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (74106, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit (New England Biolabs, lpswich, MA) and 51bp-reads paired-end sequencing was performed on a HiSeq 6000 platform (Illumina). In total, ~266 million reads were generated with an average of 38 million paired-reads per sample.

treatment_protocol: At 80% confluence, cells were infected with Ad-shlacZ or Ad-shKLF1 for 48 hours.

value: primary aortic endothelial cells

tag: passage

value: Ad-shKLF11 (10MOI)


title: HR51_24h_A


title: ABE8e-dCas_Primary_Hepatocytes_Rep3

value: tail vein


title: untagged_hybrid-2

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to the C. albicans and C. dubliniensis genome using Bowtie 2 with default parameters. Reads that aligned to both genomes were subsequently filtered out.
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz
Supplementary_files_format_and_content: summits.txt files have genes that have a peak detected by MACS2 in both replicates.
enrich_mod.txt files have the maximum fold enrichment between tagged and untagged control experiment for each upstream intergenic region in the genome.

organism: Candida albicans x Candida dubliniensis

source_name: hybrid a/alpha cell

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider 1% glucose at 37°C and 200 rpm samples were harvested.

value: Spider 1% glucose


title: Ad-shKLF11_3


title: ABE8e-dCas_Liver_Rep3


title: HR51_18h_C

value: pupae (18h after puparium formation)


title: Ad-shKLF11_2


title: HR51_18h_B

value: Brain


title: ABE8e-dCas_Primary_Hepatocytes_Rep2


title: untagged_hybrid-1


title: Cd_Ndt80_hybrid-2

description:
ChIPspglu_II_CEM309
samples for processed files: ChIPspglu_II_CEM309 - ChIPspglu_II_CEM310
CEM309-Calb.summits.txt
CEM309-Calb.enrich_mod.txt
CEM309-Cdub.summits.txt
CEM309-Cdub.enrich_mod.txt

value: C. dubliniensis Ndt80

value: c-myc


title: Ad-shKLF11_1


title: HR51_18h_A

value: DsRed +

value: gamma neurons


title: ABE8e-dCas_Liver_Rep2

value: AAV-mediated delivery


title: Cd_Ndt80_hybrid-1

description:
ChIPspglu_I_CEM309
samples for processed files: ChIPspglu_I_CEM309 - ChIPspglu_I_CEM310
CEM309-Calb.summits.txt
CEM309-Calb.enrich_mod.txt
CEM309-Cdub.summits.txt
CEM309-Cdub.enrich_mod.txt

value: biofilm

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Ad-shlacZ_3

value: Ad-shlacZ (10MOI)


title: HR51_12h_C

value: pupae (12h after puparium formation)


title: Ad-shlacZ_2


title: ABE8e-dCas_Primary_Hepatocytes_Rep1

value: targeted amplicon sequencing

value: base-edited PCSK9


title: Ca_Ndt80_hybrid-2

description:
ChIPspglu_II_CEM308
samples for processed files: ChIPspglu_II_CEM308 - ChIPspglu_II_CEM310
CEM308-Calb.summits.txt
CEM308-Calb.enrich_mod.txt
CEM308-Cdub.summits.txt
CEM308-Cdub.enrich_mod.txt

value: C. albicans Ndt80


title: ABE8e-dCas_Liver_Rep1


title: HR51_12h_A


title: Ad-shlacZ_1

value: primary aortic endothelial cells


title: HR51_12h_B


title: Ca_Ndt80_hybrid-1

description:
ChIPspglu_I_CEM308
samples for processed files: ChIPspglu_I_CEM308 - ChIPspglu_I_CEM310
CEM308-Calb.summits.txt
CEM308-Calb.enrich_mod.txt
CEM308-Cdub.summits.txt
CEM308-Cdub.enrich_mod.txt


title: 26-Nickel

status: Public on Apr 12 2021

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

hyb_protocol: Labeled material was hybridized to Affymetrix GeneChip Human PrimeView arrays as described in the Affymetrix GeneChip 3’ IVT Express Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: Scanning was performed using an Affymetrix GeneChip Scanner 3000 7G

data_processing:
A custom cdf was used - primeviewhsentrezgaltrabio183465.cdf.
Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the variance stabilization normalization followed by a quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach

source_name: Biopsy from skin treated with nickel

label_protocol: Total RNA from each sample was labeled as described in the Affymetrix GeneChip 3’ IVT Express Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from skin biopsies using Qiagen RNeasy Mini Kit (Courtaboeuf, France) and contaminating DNA was removed using  DNA-FreeTM DNA Removal kit (Invitrogen, Cergy-Pontoise, France)

tag: donor

tag: compound

value: Nickel

tag: reaction grade

value: Skin


title: 25-SLS

source_name: Biopsy from skin treated with sls

value: SLS


title: 28-Nonanoic acid

source_name: Biopsy from skin treated with nonanoic acid

value: Nonanoic acid


title: 26-Petrolatum

source_name: Biopsy from skin treated with petrolatum

value: Petrolatum


title: 24-Methylisothiazolinone

source_name: Biopsy from skin treated with methylisothiazolinone

value: Methylisothiazolinone


title: 22-Methylisothiazolinone


title: 28-Linalool hydroperoxide

source_name: Biopsy from skin treated with linalool hydroperoxide

value: Linalool hydroperoxide


title: 25-Petrolatum


title: 23-Linalool hydroperoxide


title: 27-Isopropanol

source_name: Biopsy from skin treated with isopropanol

value: Isopropanol


title: 29-Isopropanol


title: 29-Nonanoic acid


title: 21-Petrolatum


title: 24-Petrolatum


title: 19-Petrolatum


title: 27-Nonanoic acid


title: 18-Methylisothiazolinone


title: 22-Petrolatum


title: 21-Linalool hydroperoxide


title: 23-Petrolatum


title: 19-Linalool hydroperoxide


title: 18-Petrolatum


title: 20-Linalool hydroperoxide


title: 20-None

source_name: Biopsy from skin treated with none


title: 17-Nickel


title: 28-None


title: 17-Petrolatum


title: 16-Petrolatum


title: 16-Nickel


title: 15-Methylisothiazolinone


title: 14-Petrolatum


title: 13-Nickel


title: 10-Cantharidin

source_name: Biopsy from skin treated with cantharidin

value: Cantharidin


title: 8-Methylisothiazolinone


title: 10-Petrolatum


title: 7-Nickel


title: 5-Petrolatum


title: 30-Nonanoic acid


title: 13-Petrolatum


title: 6-Petrolatum


title: 14-Nickel


title: 4-Cantharidin


title: 12-Linalool hydroperoxide


title: 9-Petrolatum


title: 11-Nickel


title: 9-Cantharidin


title: 15-Petrolatum


title: 8-None


title: 12-Petrolatum


title: 7-Petrolatum


title: 11-Methylisothiazolinone


title: 5-Cantharidin


title: 30-Isopropanol


title: 3-Cantharidin


title: 11-Petrolatum


title: 9-Nickel


title: 4-Petrolatum


title: 6-Linalool hydroperoxide


title: 3-Petrolatum


title: 2-Cantharidin


title: 32-SLS


title: 1-Petrolatum


title: 1-Cantharidin


title: 31-Linalool hydroperoxide


title: 34-Linalool hydroperoxide


title: 33-Nickel


title: 32-Nickel


title: 35-Petrolatum


title: 32-Petrolatum


title: 31-SLS


title: 35-Linalool hydroperoxide


title: 35-SLS


title: 34-SLS


title: 36-Petrolatum


title: 31-Petrolatum


title: 39-Petrolatum


title: 33-SLS


title: 34-Petrolatum


title: 2-Petrolatum


title: 45-None


title: 43-None


title: 44-Petrolatum


title: 37-None


title: 46-None


title: 38-None


title: 33-Petrolatum


title: 42-Petrolatum


title: 47-Petrolatum


title: 40-Petrolatum


title: 41-Petrolatum


title: scRNAseq ZHBTc4 4d +Dox

city: Jerusalem

first: Xue

last: Sun

address: Hebrew University, Givat Ram campus

department: Biochemistry department

institute: The Hebrew University of Jerusalem

data_processing:
For all single-cell and Clone-Seq samples, the cell barcode and UMI are on Read 1, and the genomic barcode  is on Read 2 without a specific position. The structure of Read 1 is: [Barcode 1 7-10 bp] GAGTGATTGCTTGTGACGCCTT[Barcode 2 8bp][UMI 5bp]
The reads were first filtered based on the presence of two sample barcode components separated by the W1 adaptor sequence in Read 1. Barcodes for each read were matched against a list of the 768 pre-determined barcodes. Although the barcode was designed to be 3 SNPs away from each other, no mismatch was allowed in barcodes. The reads were UMI filtered, and single cell fastq files were produced.
Reads split into clone barcode-specific files were aligned using Bowtie2 (v2.3.4.3, defaut parameters) and RSEM (v1.2.31) to the mouse or human reference transcriptome. Alignments from Bowtie were filtered as follows: For each read, we retained at most one alignment per gene, across all isoforms, by choosing the alignment closest to the end of the transcript.
The Illumina output was analyzed using an in-house Perl script that produced a reads matrix. The resulting matrix was analyzed in R. For bulk data analysis the transcript per million (TPM) values were used to compare libraries.
Genome_build: hg38, mm9
Supplementary_files_format_and_content: single-cell and Clone-seq data: raw counts
Supplementary_files_format_and_content: UGI shifted primer processed data files raw counts of sequences with data in three columns: Single-cell barcode (BC1+BC2), UGI, and counts.

source_name: mouse embryonic cell line

growth_protocol: For standard tissue culture, PC9 cells were grown in DMEM supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate. ZHBTc4 ESCs cells were grown on 0.1% gelatin-coated standard tissue culture dishes and maintained in ESC medium (DMEM, 15% ESC-grade FBS, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol). To maintain pluripotency, 1000 U/ml LIF and 2i (1 μM PD0325901, 3 μM CHIR99021) were added to the culture medium.   For culture in hydrogel spheres, we used PEGDT (Mn ~10,000) and MALDEX hydrogel chemistry to encapsulate cells within spheres and grew them into clones. PC9 cells were encapsulated in PEGDT/MALDEX hydrogel with no additional cell adhesion peptides or remodeling supplements. ESCs cells were encapsulated in MALDEX and cell adhesion peptides containing cell recognition motifs of the extracellular matrix (RGD) and MMP-cleavable peptide sequence. For culturing encapsulated cells into clones, 500 μl aliquots of hydrogels were grown in a standard 48-well cell culture dish well with 500 μl standard cell growth medium as described above.

extract_protocol:
Single cells and single clone transcriptomes were extracted in microfluidic droplets. For scRNA-seq experiments, cells were loaded at 200,000 cells/ml in PBS containing 10% v/v OptiPrep and maintained in suspension using a magnetic micro-stirrer bar placed within the tube. For CloneSeq experiments, around 20,000 clones were resuspended in 900 μl PBS and 100 μl OptiPrep and maintained in suspension using a magnetic micro-stirrer bar placed within the tube. The device generates monodispersed droplets with volumes in the range of 2 nl for scRNA-seq and around 4-5 nl for CloneSeq. Single cell/clone lysates were subject to reverse transcription at 50°C without purification of RNA.
Cells were barcoded using the using inDrops platform (Klein AM et al., Cell. 2015), which makes use of the CEL-Seq protocol for library construction (Hashimshony et al., Cell Reports 2011).

treatment_protocol: To assess the impact of clonal cell origin on cellular states and variation, we produced PC9 cell lines that carry genomic barcodes. We designed and produced a plasmid pool containing a UGI region of 8 bp as a genomic barcode about 600 bp upstream of the BFP polyA region. For transfection, we grew 293T cells to 80% confluency and then incubated the cells for 30 min in conditioning medium (50 ml 293T medium supplemented with 500 μl L-glutamine and 500 μl Sodium-Pyruvate). The transfection solution contained 34.5 μl TransIT®-LT1 Transfection Reagent, 1 μg transfer plasmid (psPAX.2), 7 μg VSV-G (PMD2.G), and 3.5 μg of our BFP-UGI plasmid diluted to 1.5 ml with Opti-MEM I Reduced Serum Medium. Viruses were collected after 48 h and 72 h. For virus concentration, the PEG Virus Precipitation Kit was used. For infection, PC9 cells of 50% confluency were incubated for 30 min in 1 μl polybrene in 1 ml culture medium. PC9 cells were infected with the virus at an MOI of 1. Finally, BFP-positive cells were sorted by FACS to obtain the BFP PC9 cell line containing genetic barcodes.

tag: cell line

tag: culture

value: hydrogel spheres

tag: protocol

value: scRNAseq (inDrop)

value: untreated


title: CloneSeq ZHBTc4 4d +Dox

value: CloneSeq


title: scRNAseq ZHBTc4 24h +Dox rep1

value: tissue culture


title: bulk-RNAseq ZHBTc4 +2i/LIF rep 3

value: bulkRNAseq


title: bulk-RNAseq ZHBTc4 +2i/LIF rep 2


title: 45-Piperacillin/Tazobactam

source_name: Biopsy from skin treated with piperacillin/tazobactam

value: Piperacillin/Tazobactam


title: L2 C. elegans

city: Seattle

first: Robert

last: Waterston

state: WA

address: Foege Building S-350D, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: All processed data files except gdna_neg.blacklist_filtered.cuts.bed.

data_processing:
Convert sequencing output to fastq format (bcl2fastq v 2.19.0), split and correct barcodes, and trim adapter sequences (Trimmomatic v 0.36). These steps were performed with the sc_atac_bcl2fastq.py script.
Align reads and collapse duplicates using sc_atac_justmapping_bwa.sh script with Bowtie2 v 2.3.5 and ce11 reference.
Add a terminal letter to the cell barcode sequences (V for batch1_miseq, Y for batch2_nextseq, and Z for batch3_nextseq) to avoid collisions from different sciATAC-seq runs using modify_barcodes.py script.
Merge bam alignments with Picard MergeSamFiles v 2.15.0
Remove ce11 blacklisted regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/ce11-blacklist.v2.bed.gz) with BedTools (v 2.25.0) and Samtools (v 1.9).
Identify the Tn5 cut sites by making a BED file containing 60 bp regions centered on the outer ends of all read pairs using the make_end_bed.py script.
Call peaks using MACS2 v 2.1.1, with genomic DNA negative control as the input.
Call valid cells based on read coverage using sc_atac_samespecies_individual_readcounter.py and sc_atac_individual_cellcall_plots.R.
Tally the peaks present in each cell in a sparse matrix file using BedTools v 2.25.0 and the peaks_to_bow2.py script.
Run iterative latent Dirichlet allocation (LDA) analysis with the lda_plus2.py script and using the sparse matrix as input. This script chooses a dimensionality for the LDA model, trains the LDA, clusters the cells based on the result, pools the data for the cells from each cluster, calls peaks for each cluster using MACS2, merges the peaks called on each cluster into a single list of genomic regions called as peaks in any cluster, and then generates a new sparse matrix that can be used in another round of LDA analysis. We conducted two rounds of LDA analysis, and we call the first round the "primary" round and the second the "refinement" round. Processed files are named as such based on from which round they were generated.
Make bigWig signal files from the MACS2 output for the refinement LDA analysis, and split multi-summit peaks into multiple contiguous peak regions using the expand_summits2.py script.
Make loom files containing the cells-by-peaks matrices and LDA results for each analysis.
Genome_build: ce11
Supplementary_files_format_and_content: *.cuts.bed:  BED file containing 60 bp regions centered on Tn5 cut sites.
*.indextable.txt:  Tab-delimited file listing the cell barcodes in the first column and metadata in the second column
*_peaks.bed:  MACS peak calling results merged into non-overlapping intervals with bedtools merge.
*.bow:  "Bag of words" file containing a sparse matrix representation of the cells-by-peaks matrix. Has three header lines: the first is the number of cells, the second is the number of peaks, and the third is not used and has arbitrary content. The rest of the file consists of three columns: The 1-based cell (row) index, the 1-based peak (column) index, and the binarized read count over that peak in that cell (always 1).
*.cell_name_to_topic_cluster_map.txt:  Tab-delimited file mapping cell barcodes to their cluster assignment from the topic-based clustering strategy.
*.loom:  File containing the the cells-by-peaks matrix annotated with metadata, including the LDA results, cluster assignments, and UMAP coordinates.
*.docTopic:  File containing the number of peaks in each cell that were assigned to each topic by the LDA generative process.
*.theta:  File containing the probability distribution over topcis for each cell based on the LDA generative process and taking into account the prior.
*.wordTopic:  File containing the number of times each peak was assigned to a particular topic by the LDA generative process.
*.phi:  File containing the probability distribution over peaks for each topic based on the LDA generative process and taking into account the prior.
*_control_lambda.bedgraph:  MACS2 output bedGraph file describing the input control signal.
*_treat_pileup.bedgraph:  MACS2 output bedGraph file describing the treatment signal.
*_peaks.narrowPeak:  MACS2 output showing peak calls in UCSC narrowPeak format.
*.summits_expanded.bed:  File containing the peak regions called by MACS2, but multi-summit peaks are split into multiple contiguous segments by detecting the trough regions between summits and splitting the peaks there.
*.subtract.bedgraph:  MACS2 output after using bdgcmp subtract to compare the treat_pileup.bedgraph and control_lambda.bedgraph files.
*.subtract.bw:  BigWig file representation of the subtract.bedgraph file.
*_primary_lda*:  Files pertaining to the first round of our iterative LDA analysis procedure.
*_refinement_lda*:  Files pertaining to the second round of our iterative LDA analysis procedure.
*_lda.filtered_peaks_iqr4.0_low_cells.*:  LDA input files after filtering out the low-coverage cells and the low- and high-prevalence peaks to make the LDA training more efficient.
*_lda.topic*:  Files pertaining to peak calling on the pooled data from the cluster of cells that have high probability in the specified topic.
*.split.trimmed.fastq.gz:  Raw fastq files with error-corrected cell barcodes attached to the read names, and Illumina sequencing adapter sequence trimmed from the ends of any short-insert reads.
all_sciATAC_merged.blacklist_filtered.bam:  Aligned reads from the *.split.trimmed.fastq.gz files, filtered for MAPQ > 10, passing QC filter, and mapping outside of the ENCODE ce11 blacklist regions.
README.txt:  Explains the relationships between the samples and the processed data files

organism: Caenorhabditis elegans

source_name: whole L2 nematodes

growth_protocol: Worms were bleach-synchronized for at least two rounds and grown on 150 mm agar plates at 21 C at a density of about 60,000 worms per plate.

extract_protocol:
Formaldehyde-fixed nuclei extracted from whole L2 larval worms
Worms were flash frozen, crushed into a powder to break the worms into pieces, and then fixed in 1.1% formaldehyde. Nuclei were extracted from the fixed pieces with several rounds of Dounce homogenization.
Single cell ATAC-seq libraries were generated using the sciATAC-seq protocol (Cusanovich, et al. 2015).
sciATAC-seq

tag: sample type

value: Nuclear isolation


title: 39-acetazolamide

source_name: Biopsy from skin treated with acetazolamide

value: acetazolamide


title: bulk-RNAseq ZHBTc4 +2i/LIF rep 1

tag: treatment


title: bulk-RNAseq ZHBTc4 -2i/LIF rep 3


title: 46-Amoxicillin

source_name: Biopsy from skin treated with amoxicillin

value: Amoxicillin

value: Skin


title: 41-Amoxicillin


title: 37-SLS

value: SLS


title: 38-SLS


title: bulk-RNAseq ZHBTc4 -2i/LIF rep 2


title: 36-SLS


title: 44-Amoxicillin


title: 47-SLS


title: 40-Amoxicillin


title: bulk-RNAseq ZHBTc4 -2i/LIF rep 1


title: scRNAseq ZHBTc4 24h +Dox rep2


title: 42-SLS


title: bulk-RNAseq R1 -2i/LIF 3D rep 1

data_processing:
The cell barcode and UMI are on Read 1, and the genomic barcode for sample 4 to 7 (scRNAseq barcoded PC9 2D rand, scRNAseq barcoded PC9 2D BC,scRNAseq barcoded PC9 3D rand, scRNAseq barcoded PC9 3D BC) is on Read 2 without a specific position.
The structure of Read 1 is: [Barcode 1 7-10 bp]GAGTGATTGCTTGTGACGCCTT[Barcode 2 8bp][UMI 5bp]
The reads were first filtered based on the presence of two sample barcode components separated by the W1 adaptor sequence in Read 1. Barcodes for each read were matched against a list of the 768 pre-determined cell barcodes. 384 barcodes for each of Barcode 1 and Barcode 2. Although the barcode was designed to be 3 SNPs away from each other, no mismatch was allowed in barcodes. The reads were UMI filtered, and single cell fastq files were produced.
The genomic barcodes were inserted by a lentivirus BFP reporter plasmid that contains barcode at 3' end as described in "Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq". We used the Unique Genomic Index (UGI) in the plasmid as our genomic barcode. There is no pre-determined set for it. For the analysis, we looked for the constant region contains the Barcode region as the following structure: GTCGACGGATCC[UGI 8bp]GACTTAC
Reads split into clone barcode-specific files were aligned using Bowtie2 (v2.3.4.3, defaut parameters) and RSEM (v1.2.31) to the mouse or human reference transcriptome. Alignments from Bowtie were filtered as follows: For each read, we retained at most one alignment per gene, across all isoforms, by choosing the alignment closest to the end of the transcript.
The Illumina output was analyzed using an in-house Perl script that produced a reads matrix. The resulting matrix was analyzed in R. For bulk data analysis the transcript per million (TPM) values were used to compare libraries.
Genome_build: hg38, mm9

growth_protocol: For standard tissue culture, PC9 cells were grown in DMEM supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate. R1 ESCs cells were grown on 0.1% gelatin-coated standard tissue culture dishes and maintained in ESC medium (DMEM, 15% ESC-grade FBS, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol). To maintain pluripotency, 1000 U/ml LIF and 2i (1 μM PD0325901, 3 μM CHIR99021) were added to the culture medium.   For culture in hydrogel spheres, we used PEGDT (Mn ~10,000) and MALDEX hydrogel chemistry to encapsulate cells within spheres and grew them into clones. PC9 cells were encapsulated in PEGDT/MALDEX hydrogel with no additional cell adhesion peptides or remodeling supplements. ESCs cells were encapsulated in MALDEX and cell adhesion peptides containing cell recognition motifs of the extracellular matrix (RGD) and MMP-cleavable peptide sequence. For culturing encapsulated cells into clones, 500 μl aliquots of hydrogels were grown in a standard 48-well cell culture dish well with 500 μl standard cell growth medium as described above.


title: bulk-RNAseq R1 -2i/LIF 3D rep 2


title: bulk-RNAseq R1 -2i/LIF 2D rep 1

value: standard tissue culture


title: SAH brain endothelial cells, biological rep3

city: Toronto

first: Michael

last: Tso

state: ON

address: 30 Bond St.

department: Neurosurgery

country: Canada

institute: University of Toronto

description: SAH, 3

hyb_protocol: Hybridized to Affymetrix Mouse Gene 2.0 ST Arrays for 18 h at 45 oC at 60 revolutions per minute (RPM)

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with R statistical software version 3.2.2 using the “oligo” package derived from Bioconductor version 3.2

source_name: SAH brain endothelial cells

label_protocol: Total RNA amplified with Ovation Pico WTA System V2 and 5.0 μg of the cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN)

growth_protocol: FVB/NJ, Jackson Laboratory

extract_protocol: Mouse brains extracted at 24h with removall of meninges, cerebellum, and brainstem; magnetic beads were used to deplete myelin and then isolate viable CD45-CD31+ endothelial cells; total RNA extracted via Rneasy microkit

treatment_protocol: Prechiasmatic blood injection model with 80microL blood injection vs. sham procedure with needle insertion but without blood injection

value: FVB/NJ

tag: age

value: 12 weeks old

tag: Sex

value: male

value: SAH

tag: cell type

value: brain CD45-CD31+ endothelial cells


title: 43-Amoxicillin


title: Sham brain endothelial cells, biological rep3

description: Sham, 4

source_name: Sham brain endothelial cells

value: Sham


title: Sham brain endothelial cells, biological rep2

description: Sham, 3


title: Sham brain endothelial cells, biological rep1

description: Sham, 1


title: R3__cas1_flg22_12h

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
We cleaned the paired-end reads by Trimimomatic (version 0.36). After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Cleaned reads were mapped to the genome sequence by HISAT (version 2.1.0) with default parameters.
Number of reads that were mapped to each gene was calculated with the htseq-count script in HTSeq (version 0.9.1)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene

organism: Arabidopsis thaliana

source_name: A. thaliana Col-0 mutant

growth_protocol: ten-day-old Arabidopsis seedlings grown on ½ MS agar plates under long-day conditions (16/8h day-light)

extract_protocol:
Qiagen Plant mRNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: transfer to ½ MS liquid for elicitation with the bacterial peptide elicitor flg22 (1 µM, 12 h) vs mock (water, 12h)

tag: experimental conditions

value: flg22 1uM 12h. 16/8h day-light on 1/2 MS

tag: preparation kit

value: Qiagen Plant mRNeasy mini

tag: elution

value: nuclease-free water


title: R1__cas1_flg22_12h


title: R4__cas1_flg22_12h


title: SAH brain endothelial cells, biological rep2

description: SAH, 2

tag: strain


title: R2__cas1_flg22_12h


title: Sham brain endothelial cells, biological rep4

description: Sham, 6


title: SAH brain endothelial cells, biological rep4

description: SAH, 6


title: R4__cas1_mock_12h

value: MOCK 12h. 16/8h day-light on 1/2 MS


title: bulk-RNAseq R1 -2i/LIF 2D rep 2

value: bulkRNAseq

value: untreated


title: SAH brain endothelial cells, biological rep1

description: SAH, 1


title: R3__cas1_mock_12h


title: LysoDC_C5aR_Minus 2

city: Jeonju-si, Jeollabuk-do,

first: Saehae

last: Kim

address: 567 Baekje-daero, Deokjin-gu,

department: Molecular biology

country: South Korea

institute: Jeonbuk National University

description: Gene expression data from LysoDC_C5aR_Minus

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools(APT).
Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

source_name: Peyer's patch LysoDC_C6aR_Minus

label_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip WT Pico reagent Kit). cDNA was synthesized using the GeneChip WT Pico Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: PPs were incubated for 20 min at 37°C with 10 mM ethylenediaminetetraacetic acid buffer and then digested for 45 min at 37°C with collagenase D (Roche)/DNase I (Sigma). After removing dead cells using a dead cell removal kit CD11c+ cells were enriched using anti-mouse CD11c microbeads according to the manufacturer’s instructions.

extract_protocol: Total RNA from sorted cells was prepared using an RNeasy PLUS Micro kit according to the manufacturer’s protocols (Qiagen).

treatment_protocol: Multiparameter flow cytometry was performed using a FACSAria III (BD Biosciences); cell sorting was performed using FACSAria III. The following antibodies (obtained from BioLegend, BD Bioscience, and Thermo Fisher Scientific) were used to analyze cell surface markers: CD11c (N418), SIRP(P84), BST2 (eBio927), C5aR (20/70), CD4 (RM4-5), and MHCII (2G9).

tag: tissue

value: Peyer patch


title: R2__cas1_mock_12h


title: LysoDC_C5aR_Minus 1

source_name: Peyer's patch LysoDC_C5aR_Minus


title: R1__cas1_mock_12h


title: LysoDC_C5aR_ Plus 3

description: Gene expression data from LysoDC_C5aR_Plus

source_name: Peyer's patch LysoDC_C5aR_Plus


title: R4_C4G2A_L7.7_flg22_12h

source_name: A. thaliana Col-0 Transgenic line


title: LysoMac3

description: Gene expression data from LysoMac

source_name: Peyer's patch LysoMac


title: LysoDC_C5aR_ Plus 2


title: LNCaP_shDouble_R1881_Rep2

city: Aurora

first: Lauren

last: Jillson

state: Colorado

address: 12801 E 17th Avenue, Room L18-6213, Mail stop 8303

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina HiSEQ 2000 High-throughput mode using V3 Chemistry, PE100
Libraries were prepared with the Illumina TruSEQ Stranded Total RNA with Ribo-Zero TM library preparation kit.
Gene expression was quantified using default parameter of RSEM (v1.2.1) with Bowtie2 (v2.1.0) as the read aligning program. Reads were aligned to hg19 RefSeq annotated genes
Differential gene expression was calculated using EBSeq (v1.1.5)
Genome_build: hg19
Supplementary_files_format_and_content: The raw transcript counts (LNCaP_compiled_raw) and RSEM-normalized values (LNCaP_compiled_normalized)  below contain compiled data for each cell type delineated by column headers.

source_name: LNCaP prostate cancer cell line

growth_protocol: LNCaP cells are maintained on uncoated culture dishes in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. LNCaP cells were previously engineered with the following shRNAs using lentivirus transduction: shControl (puromycin and neomycin constructs), shMAP3K7 (puromycin), shCHD1 (neomycin). This generated 4 groups: 1. shControl(puro/neo), 2. shMAP3K7(puro)/shControl (neo), 3. shCHD1(neo)/shControl(puro), and 4. shMAP3K7(puro)/shCHD1(neo).

extract_protocol:
After the above 4 hour treatments, total RNA was collected using the 5Prime Perfect RNA Cell Kit (Fisher Scientific) according to the manufacturer's protocol, including the optional DNAase treatment
After quality control, RNA samples were enriched for mRNA using oligo(dT) beads, fragmented for a 250-300 bp target range, then cDNA synthesis using random hexamer primers, second strand synthesis is performed using dNTPs, RNAas H and DNA polymerase I in Illumina synthesis buffer, Illumina sequencing adapters, then the double-stranded cDNA library is size selected and PCR enriched.

treatment_protocol: These 4 LNCaP cell types were plated on 6cm culture dishes in the above culture medium and left for 2 days. They were then hormone deprived by culturing in RPMI 1640 medium (-phenol red) with 10% charcoal-stripped serum and 1% penicillin/streptomycin for 3 additional days, reaching 80% confluency. Then they were treated with either vehicle (0.1% EtOH) or 1nM of the synthetic androgen R1881 for 4 hours beofre collection of RNA.

value: LNCaP

tag: genotype

value: shMAP3K7_puro, shCHD1_neo

value: 1nM R1881, 4 hours

tag: passage


title: LNCaP_shDouble_R1881_Rep3


title: LysoMac2

description: Gene expression data from LysoMac


title: LysoMac1

description: Gene expression data from LysoMac


title: LNCaP_shDouble_EtOH_Rep3

value: 0.1% Ethanol, 4hours


title: LNCaP_shDouble_EtOH_Rep2


title: R2_C4G2A_L7.7_flg22_12h


title: R4_C4G2A_L7.7_mock_12h


title: R3_C4G2A_L7.7_mock_12h


title: LysoDC_C5aR_Minus 3

source_name: Peyer's patch LysoDC_C7aR_Minus


title: LysoDC_C5aR_ Plus 1


title: LNCaP_shCHD1_R1881_Rep3

value: shCHD1_neo, shControl_puro


title: LNCaP_shDouble_R1881_Rep1


title: LNCaP_shCHD1_R1881_Rep2


title: LNCaP_shDouble_EtOH_Rep1


title: R3_C4G2A_L7.7_flg22_12h


title: R1_C4G2A_L7.7_flg22_12h


title: R1_C4G2A_L7.7_mock_12h


title: R2_C4G2A_L7.7_mock_12h


title: R4_C4G2A_L1.3_flg22_12h


title: R2_C4G2A_L1.3_flg22_12h


title: R1_C4G2A_L1.3_flg22_12h


title: R3_C4G2A_L1.3_flg22_12h


title: R4_C4G2A_L1.3_mock_12h


title: LNCaP_shCHD1_R1881_Rep1


title: R2_C4G2A_L1.3_mock_12h


title: R1_C4G2A_L1.3_mock_12h


title: R3_Col-0_flg22_12h

source_name: A. thaliana Col-0 wild-type


title: R2_Col-0_flg22_12h


title: R4_Col-0_flg22_12h


title: LNCaP_shCHD1_EtOH_Rep1


title: LNCaP_shMAP3K7_R1881_Rep1

value: shMAP3K7_puro, shControl_neo


title: LNCaP_shMAP3K7_R1881_Rep3


title: R1_Col-0_flg22_12h


title: LNCaP_shControl_R1881_Rep1

value: shControl_puro, shControl_neo


title: LNCaP_shControl_R1881_Rep2


title: LNCaP_shMAP3K7_EtOH_Rep2


title: LNCaP_shControl_EtOH_Rep3


title: LNCaP_shControl_EtOH_Rep2


title: LNCaP_shMAP3K7_R1881_Rep2


title: LNCaP_shMAP3K7_EtOH_Rep1


title: LNCaP_shControl_R1881_Rep3


title: LNCaP_shCHD1_EtOH_Rep2


title: LNCaP_shCHD1_EtOH_Rep3


title: R4_Col-0_mock_12h


title: LNCaP_shControl_EtOH_Rep1


title: LNCaP_shMAP3K7_EtOH_Rep3


title: R3_C4G2A_L1.3_mock_12h


title: R2_Col-0_mock_12h


title: shDouble_EtOH_INPUT

data_processing:
Samples were pooled and sequenced on Illumina HiSEQ 2000 High-throughput mode using V3 Chemistry, PE100
The fastq file quality was accessed using FastQC and MultiQC
Illumina adapters and low-quality reads were filtered out using BBDuk
Bowtie2 (v.2.3.4.3) was used to align reads to the hg38 reference human genome. Samtools (v.1.9) was used to select the mapped reads.
Optical and PCR duplicates were removed using Picard MarkDuplicates tool. The same number of reads for all samples was randomly extracted using samtools view
Peaks were called using MACS2 (v2.1.1) with default parameters.
Igvtools toTDF was used to create tdf files.
Genome_build: hg38
Supplementary_files_format_and_content: tdf files

extract_protocol:
Cells were crosslinked, lysates were sonicated, precleared, and incubated with 10ug antibody (AR N-20) and agarose beads. Aliquots of precleared lysates were taken as input controls before antibody incubation. Beads were extensivley washed and protein-antibody complexes were eluted and reverse cross-linked. Supernatants were treated with Proteinase K, RNAase A. DNA was purified with the Wizard SV Gel and PCR Clean-Up System (Promega) and meausured with the Qubit dsDNA HS kit (Invitrogen).
1 ng of ChIP or input DNA per sample was used for library construction following NuGEN DNA-Seq library preperpation instructions.

treatment_protocol: These 4 LNCaP cell types were plated on 15cm culture dishes in the above culture medium and left for 2 days. They were then hormone deprived by culturing in RPMI 1640 medium (-phenol red) with 10% charcoal-stripped serum and 1% penicillin/streptomycin for 3 additional days, reaching 80% confluency. Then they were treated with either vehicle (0.1% EtOH) or 1nM of the synthetic androgen R1881 for 4 hours before initiating ChIP protocol. Each group was performed in triplicate, and the triplicate samples were pooled for sequencing.

tag: chip antibody


title: R1_Col-0_mock_12h


title: shDouble_R1881_INPUT


title: shCHD1_R1881_INPUT


title: shCHD1_EtOH_INPUT


title: shMAP3K7_R1881_INPUT


title: shMAP3K7_EtOH_INPUT


title: shControl_R1881_INPUT


title: macrophage haplo2_LPS_RNAseq

city: Irvine

first: Minji

last: Byun

state: California

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

data_processing:
Transcript quantification was performed with Salmon based on GENCODE Human release 33.
tximeta was used to assemble estimated count.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Macrophages

growth_protocol: Culture conditions for hESCs and the macrophage differentiation protocol can be found in the associated publication.

extract_protocol:
Total RNA was extracted using Zymo Quick-RNA microprep kit.
Illumina TruSeq RNA Library Preparation Kits

treatment_protocol: Macrophages were treated with either PBS or LPS (100ng/ml) for 4 hours.

value: hESC-derived macrophages

value: LPS-treated


title: macrophage null1_LPS_RNAseq


title: shControl_EtOH_INPUT


title: macrophage null2_LPS_RNAseq


title: macrophage haplo1_LPS_RNAseq


title: macrophage haplo3_LPS_RNAseq


title: R3_Col-0_mock_12h


title: macrophage WT2_LPS_RNAseq

value: wild type


title: shCHD1_EtOH

value: AR N-20 (Santa Cruz #sc-816)


title: shCHD1_R1881


title: macrophage null3_mock_RNAseq

value: PBS-treated


title: macrophage WT1_LPS_RNAseq


title: macrophage null2_mock_RNAseq


title: shMAP3K7_R1881


title: shMAP3K7_EtOH


title: shControl_R1881


title: shControl_EtOH


title: macrophage null3_LPS_RNAseq


title: macrophage haplo2_mock_RNAseq


title: macrophage null1_mock_RNAseq


title: macrophage haplo3_mock_RNAseq


title: RNAseq_PHF19_sh2_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description:
RNA-seq experiment
DESeq2_output_shCT12_Vs_sh1sh212.txt.gz

data_processing:
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
RNA-seq analysis: Analysis of differential expression with DESeq2 (PubMed ID 25516281) where shCT samples are labelled as Controls and sh1/sh2 samples as Mutants.
Genome_build: hg19
Supplementary_files_format_and_content: BEDGRAPH

source_name: immortalized myelogenous leukemia cell line

growth_protocol: K562 cells were cultured at 37C and 5% of CO2 in RPMI medium supplemented with 10% of fetal bovine serum

extract_protocol:
(RNA-seq) RNA was extracted with the RNeasy kit (Qiagen) following manufacturer's instruction
Libraries were prepared according to Illumina instructions.

value: PHF19 long isoform knockdown


title: macrophage haplo1_mock_RNAseq


title: shDouble_EtOH


title: RNAseq_PHF19_sh2_R1


title: macrophage WT3_LPS_RNAseq


title: shDouble_R1881


title: RNAseq_PHF19_sh1_R2


title: macrophage WT1_mock_RNAseq


title: RNAseq_PHF19_sh1_R1


title: macrophage WT2_mock_RNAseq


title: RNAseq_PHF19_shCT_R1

value: control


title: 37-Amoxicillin

tag: donor

tag: compound

value: Amoxicillin

tag: reaction grade

value: Skin


title: macrophage null2_WGBS

data_processing:
Quality- and adaptor-trimmed raw sequences were aligned to GRCh38/hg38 primary genome and deduplicated using bismark.
CpG methylation data was extracted using the bismark_methylation_extractor.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bismark coverage files contain chromosome, start position, end position, methylation percentage, count methylated, and count unmethylated for each position.

source_name: macrophages

extract_protocol:
Genomic DNA was extracted and purified from cells using Zymo Quick-DNA microprep kit according to standard instructions.
Bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) following the manufacturer’s protocol.


title: RNAseq_PHF19_shCT_R2

tag: cell line


title: macrophage null1_WGBS


title: ChIPseq_MTF2_sh2

description: ChIP-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection (PHF19_shCT against PHF19_sh2 and MTF2 samples against IgG) was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)

extract_protocol:
(ChIP-seq) Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit from Active Motif (#53040) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.

value: MTF2 (Proteintech 16208-1-AP) / Drosophila H2Av (Active Motif #61686)


title: macrophage haplo3_WGBS


title: macrophage haplo2_WGBS


title: ChIPseq_MTF2_shCT

description: ChIP-seq experiment


title: ChIPseq_PHF19_sh2

description: ChIP-seq experiment

value: PHF19 (Cell Signaling #77271) / Drosophila H2Av (Active Motif #61686)


title: macrophage haplo1_WGBS


title: ChIPseq_PHF19_sh1

description: ChIP-seq experiment


title: ChIPseq_PHF19_shCT

description: ChIP-seq experiment


title: macrophage WT1_WGBS


title: macrophage WT2_WGBS


title: K4me2_H1_r1_(20190828_K4me2_H1_r1)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: scCUT&Tag (iCell8) for native nuclei from H1 hESC

data_processing:
Genome_build: UCSC HG38
A. iCell8 system: 1. We used a custom python script to demultiplex and annotate fastq reads in the following format: Antibody_CellType_Rep_Cell#, e.g K27me3_K562_r1_54. 2. we used Bowtie2 2.3.4.3 with options --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700 to map the paired-end 25bp reads to HG38 of Homo sapiens genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a fragment bed files <chr> <start> <stop> <barcode> <duplicateCount>. Custom software to analyse these files is available from https://github.com/Henikoff/scCUT-Tag. B. 10X system: Cell Ranger ATAC v1.1 from 10X company with default parameters was used to do the demultiplexing, alignment to HG38 and read quantification.

source_name: CUT&TAG

tag: antibody

value: H3K4me2, Upstate (Millipore), Cat# 07-030; Lot# 26335

value: hESC


title: macrophage WT3_WGBS


title: macrophage WT3_mock_RNAseq

tag: treatment


title: K27me3_H5DE_r1_(20190624_K27me3_H5DE_r1)

description: scCUT&Tag (iCell8) for native nuclei from a directed differentiation time-coarse of H1 hESC to Endoderm

value: H3K27me3, Cell Signaling Technology, Cat# 9733; Lot# 8

value: hESC to Endoderm (Day 5, Rep 1)


title: ChIPseq_IgG_shCT

description: ChIP-seq experiment


title: macrophage null3_WGBS


title: K27me3_H5DE_r2_(20190910_K27me3_H5DE_r2)

value: hESC to Endoderm (Day 5, Rep 2)


title: K27me3_H3DE_r1_(20190624_K27me3_H3DE_r1)

value: hESC to Endoderm (Day 3, Rep 1)


title: K27me3_H4DE_r2_(20190910_K27me3_H4DE_r2)

value: hESC to Endoderm (Day 4, Rep 2)


title: K27me3_H4DE_r1_(20190624_K27me3_H4DE_r1)

value: hESC to Endoderm (Day 4, Rep 1)


title: K27me3_H2DE_r2_(20190910_K27me3_H2DE_r2)

value: hESC to Endoderm (Day 2, Rep 2)


title: K27me3_H2DE_r1_(20190624_K27me3_H2DE_r1)

value: hESC to Endoderm (Day 2, Rep 1)


title: K27me3_H1_r1_(20190829_K27me3_H1_r3)


title: K27me3_H1DE_r2_(20190910_K27me3_H1DE_r2)

value: hESC to Endoderm (Day 1, Rep 2)


title: K27me3_H1DE_r1_(20190624_K27me3_H1DE_r1)

value: hESC to Endoderm (Day 1, Rep 1)


title: N6_SUPERNATANT_SALM_INFECTED

city: Chennai

first: Areejit

last: Samal

state: Tamil Nadu

address: 4th Cross Road

department: Computational Biology

country: India

institute: The Institute of Mathematical Sciences (IMSc)

description: small RNA fraction

data_processing:
Quality of the reads was analyzed using FastQC (version 0.11.8).
The reads were trimmed and adapter sequences were removed using Trimmomatic (version 0.38).
The reads in fastq format were converted to fasta format using fastq_to_fasta commands in the FASTX Toolkit (version 0.0.13).
Further read processing, including polyA-tail removal, size filtering (minimal length 12 nt after clipping), alignment of the reads, computation of alignment statistics and annotation, was performed using the READemption pipeline version 0.4.3 with default parameters, with Segemehl version 0.2.0. Reads were mapped against the mature miRNA sequences provided by miRBase (release 22).
Quality of the reads was analyzed using FastQC (version 0.11.8).
The reads were trimmed and adapter sequences were removed using Trimmomatic (version 0.38).
Genome_build: miRBase release 22
Supplementary_files_format_and_content: Tab separated files with read counts.

source_name: HeLa cells

growth_protocol: HeLa-229 cells grown in standard conditions (DMEM 1 g/L glucose (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom), maintained in a 5% CO2, humidified atmosphere, at 37°C)

extract_protocol:
For total RNA isolation, including small RNA fraction, cells were lysed in TRIzol (Invitrogen, 15596026) and RNA was extracted by phenol-chloroform followed by isopropanol precipitation.
Library preparation and deep-sequencing was performed by the EMBL Genomics Core Facility. Briefly, RNA integrity was checked using the RNA Nano 6000 Assay Kit (Agilent Technologies, 5067-1511) in a Bioanalyzer 2100 system (Agilent Technologies), and concentration was measured with Qubit RNA Assay Kit (Invitrogen, Q10211) in a Qubit 2.0 Flurometer (Invitrogen). Small RNA-seq libraries were prepared manually from 250 ng of total RNA using the NEBNext Multiplex Small RNA Library Prep kit (New England Biolabs, E7300L). Obtained libraries that passed the QC step, which was assessed on the Agilent Bioanalyzer system, were pooled in equimolar amounts. 10 pM solution of each pool of libraries was loaded on the Illumina sequencer HiSeq2500 and sequenced uni-directionally, generating ~190 million reads per run, each 62 bases long.

treatment_protocol: HeLa cells were treated with the secretome of mock-treated cells or Salmonella infected cells (MOI 100, 20hpi). Twenty-four hours after treatment cells were collected.

value: Human epithelial HeLa-229 (ATCC CCL-2.1)

value: HeLa-229 (ATCC CCL-2.1)

value: treated with secretome of Salmonella infected cells


title: RNA_NELFBKO_2

city: Boston

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
HI.5165.002.UDI0075_i7---UDI0075_i5.Ott-JD_K-2
processed data file: deseq2results_nelfbko_vs_wt.tsv

data_processing:
PRO-seq reads were trimmed to 41bp and subsequently trimmed via cutadapt v1.14 to remove adapters: --match-read-wildcards -m 20 -q 10
PRO-seq Read 1 was aligned (single-end) using bowtie v1.2.2: -v 2 -p 6 --best --un
RNA-seq reads were quantified using kallisto v0.45.1: -b 30 --rf-stranded --genomebam --gtf --chromosomes -t 6
RNA-seq differential expression statistics were computed via tximport v1.12.3 and DESeq2 v1.24.0
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; differential expression matrix

growth_protocol: Myoblasts were harvested from WT and NELF-BscKO mice, then grown in primary myoblast growth culture for 3 days.

extract_protocol:
Nuclear run-on using permeabilized cells.  Biotin-11-NTPs were incorporated into nascent transcripts during run-on and total RNA was isolated using a column based total RNA isolation kit.
PRO-seq (Precision nuclear run-on).  Biotinylated RNA from nuclear run-on was fragmented before enrichment on streptavidin magnetic beads. Illumina compatible ssRNA adapters were ligated sequentially to the RNA ends.

treatment_protocol: Myoblasts were treated with 4-hydroxytamoxifen during growth which was replenished at 24 hour intervals. This allows activation of CreERT2 for excision of floxed sites.

tag: genotype/variation

value: NELF-BscKO

value: muscle satellite cells


title: RNA_NELFBKO_1

description:
HI.5165.002.UDI0074_i7---UDI0074_i5.Ott-JD_K-1
processed data file: deseq2results_nelfbko_vs_wt.tsv


title: N3_SUPERNATANT_MOCK

description: small RNA fraction

value: treated with secretome of mock-treated cells


title: RNA_WT_2

description:
HI.5165.002.UDI0077_i7---UDI0077_i5.Ott-JD_W-2
processed data file: deseq2results_nelfbko_vs_wt.tsv

value: wild type


title: NP+ B cells

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

data_processing:
The Cell Ranger Single Cell Software Suite 4.0.0 was used to perform sample demultiplexing, barcode processing, and single cell gene counting (http://software.10xgenomics.com/single-cell/overview/welcome).
Genome_build: mm10
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

source_name: NP+B220+ splenocytes

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions.  cDNA libraries were constructed using Chromium Single Cell 5' Library Construction Kit v1.0.
Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

value: NP+B220+ splenocytes

tag: days post-immunization

value: NP-KLH


title: N5_SUPERNATANT_MOCK

description: small RNA fraction

tag: cell type


title: N4_SUPERNATANT_SALM_INFECTED

description: small RNA fraction


title: N1_SUPERNATANT_MOCK

description: small RNA fraction


title: N2_SUPERNATANT_SALM_INFECTED

description: small RNA fraction


title: Male RORasg/sg mouse heart_rep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: RNA samples from male RORasg/sg mouse

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

label_protocol: Seventy nanograms (70 ng) of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System and 5 ug of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

growth_protocol: Mice were weaned at 3 weeks and fed Normal diet (NIH31).

extract_protocol: Ambion RNAqous mircro kit

treatment_protocol: Nothing was treated

tag: age

value: 3 - 4 month old

value: heart


title: Male WT mouse heart_rep5

description: RNA samples from male WT mouse


title: Male RORasg/sg mouse heart_rep2

description: RNA samples from male RORasg/sg mouse


title: Male RORasg/sg mouse heart_rep3

description: RNA samples from male RORasg/sg mouse


title: Male RORasg/sg mouse heart_rep4

description: RNA samples from male RORasg/sg mouse


title: K27me3_H3DE_r2_(20190910_K27me3_H3DE_r2)

value: H3K27me3, Cell Signaling Technology, Cat# 9733; Lot# 8

value: hESC to Endoderm (Day 3, Rep 2)


title: Male WT mouse heart_rep3

description: RNA samples from male WT mouse


title: Male WT mouse heart_rep4

description: RNA samples from male WT mouse


title: RNA_WT_1

description:
HI.5165.002.UDI0076_i7---UDI0076_i5.Ott-JD_W-1
processed data file: deseq2results_nelfbko_vs_wt.tsv


title: Male WT mouse heart_rep1

description: RNA samples from male WT mouse


title: S12_BYSTANDER

description: small RNA fraction

treatment_protocol: HeLa cells were were infected  with Salmonella (MOI 100) . At 20 h after infection, cells were trypsinized and collected in PBS. Sorting of the GFP-negative cells (bystander) and GFP-positive (Salmonella positive) cells was performed using a FACSAria III flow cytometer (BD Biosciences) based on the signal intensity from the FITC-A channel. Mock-treated cells were also subjected to the same procedure.

value: infected with Salmonella (bystander cells)


title: S11_SALMONELLA_POSITIVE

description: small RNA fraction

value: infected with Salmonella (Salmonella positive cells)


title: Male WT mouse heart_rep2

description: RNA samples from male WT mouse


title: IMC Mice M1 with 5TGM1 CALR KO treated with BTZ

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: 5TGM1 WT Tumor S1 with CALR KO treated with BTZ

data_processing:
For in-vitro study paired end reads were aligned to human ref genome hg19 and quantified using STAR aligner. All differential gene expression analysis were done using DESeq2.
For in-vivo study single end reads were aligned to mus musculus ref genome MM9 and quantified using STAR aligner. All differential gene expression analysis were done using DESeq2.
Genome_build: hg19 for in-vitro and MM9 for in-vivo study
Supplementary_files_format_and_content: Quantified counts with STAR in text file

source_name: Mice injected with 5TGM1 CALR KO

growth_protocol: For in vitro study, AMO1 WT and STING KO cell lines were cultured in in RPMI/1640 media containing 10% fetal bovine serum (FBS) 2 μmol/L glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin. For in vivo study, 5TGM1 WT and CALR KO cell lines were cultured in in Iscove's Modified Dulbecco's Media (IMDM) media supplemented with 10% FBS and 1% penicillin-streptomycin. C57BL/KaLwRijHsd mice were subcutaneously injected with 1x10 6 5TGM1 either WT or CalrKO cells in PBS.

extract_protocol: RNeasy kit from Qiagen

treatment_protocol: For in vitro study, AMO1 WT and STING KO cells were treated overnight with 5nM of BTZ. Foi in vivo study, mice were treated with BTZ that was administered intra peritoneally 0.5 mg/kg

value: 5TGM1 tumor


title: IMC Mice M2 with 5TGM1 CALR KO treated with BTZ

description: 5TGM1 WT Tumor S2 with CALR KO treated with BTZ


title: IMC Mice M3 with 5TGM1 CALR KO treated with BTZ

description: 5TGM1 WT Tumor S3 with CALR KO treated with BTZ


title: S10_TOTAL

description: small RNA fraction

value: infected with Salmonella (total population)


title: IMC Mice M3 with 5TGM1 CALR KO CNT

description: 5TGM1 WT Tumor S3 with CALR KO


title: IMC Mice M2 with 5TGM1 CALR KO CNT

description: 5TGM1 WT Tumor S2 with CALR KO


title: S9_MOCK

description: small RNA fraction

value: Human epithelial HeLa-229 (ATCC CCL-2.1)

value: mock-treated


title: IMC Mice M1 with 5TGM1 CALR KO CNT

description: 5TGM1 WT Tumor S1 with CALR KO


title: S8_BYSTANDER

description: small RNA fraction

value: HeLa-229 (ATCC CCL-2.1)


title: IMC Mice M3 with 5TGM1 WT treated with BTZ

description: 5TGM1 WT Tumor S3 treated with BTZ

source_name: Mice injected with 5TGM1 WT


title: S7_SALMONELLA_POSITIVE

description: small RNA fraction


title: S6_TOTAL

description: small RNA fraction


title: IMC Mice M2 with 5TGM1 WT treated with BTZ

description: 5TGM1 WT Tumor S2 treated with BTZ


title: S5_MOCK

description: small RNA fraction


title: IMC Mice M1 with 5TGM1 WT treated with BTZ

description: 5TGM1 WT Tumor S1 treated with BTZ


title: CNT IMC Mice M3 with 5TGM1 WT

description: 5TGM1 WT Tumor S3


title: S3_SALMONELLA_POSITIVE

description: small RNA fraction


title: S2_TOTAL

description: small RNA fraction


title: S1_MOCK

description: small RNA fraction


title: CNT IMC Mice M2 with 5TGM1 WT

description: 5TGM1 WT Tumor S2


title: CA10_E2F1_3

description: small RNA fraction

treatment_protocol: siRNAs were transfected into HeLa-229 cells using a standard reverse transfection protocol (Lipofectamine RNAiMAX, Life Technologies), at a final siRNA concentration of 5 nM. Cells were collected 72h pos-transfection.

value: transfected with E2F1 siRNA


title: CA9_E2F1_2

description: small RNA fraction


title: S4_BYSTANDER

description: small RNA fraction


title: Naive_MF

city: New York

first: Maria

last: Casanova Acebes

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
Gene expression libraries were aligned to the mm10 reference transcriptome and count matrices were generated using the default Cell Ranger v2 workflow, using the “raw” matrix output.
Genome_build: mm10

source_name: Monocyte and macrophages from murine lungs

extract_protocol:
Single cell suspensions were obtained from lung followed by digestion with collagenase IV 0.25mg/ml (Sigma) at 37°C for 30min followed by passing through a 70mm cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 2min at room temperature.
For each mouse scRNAseq sample, 8,500 monocytes and macrophages were sorted as CD45+LINNEG (CD3/CD19/NKP46) CD11B+LY6GNEG and encapsulated using the 10X Chromium 3’ v2 chemistry kit according to manufacturer instructions. Sequencing libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed by CyberGreen qPCR library quantification assay (KAPA). Samples were sequenced on an Illumina Nextseq 550 using the 75-cycle kit to a depth of 100 million reads per library.

tag: strain background

value: Naive

value: lung

value: Enriched sorted monocytes and macrophages


title: Single celll RNA sequencing data

data_processing:
Basecalls performed using Cellranger v4.0.0
Single cell reads were aligned to the mm10 genome assembly using Cellranger v4.0.0
Data were filtered by EmptyDrops method
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix generated by Cellranger v4.0.0

source_name: CD11chiMHChiSIRPa+ Peyer's patch cells

extract_protocol:
PPs were incubated for 20 min at 37°C with 10 mM ethylenediaminetetraacetic acid buffer and then digested for 45 min at 37°C with collagenase D/DNase I. After removing dead cells using a dead cell removal kit CD11c+ or CD8+ cells were enriched using anti-mouse CD11c microbeads or a CD8+ T cell isolation kit
We utilized the 10X Genomics Chromium Instrument and cDNA synthesis kit (10x Genomics) to generate a barcoded cDNA library for single cell RNA-sequencing from approximately 8,500 cells. cDNA library quality was determined using an Agilent Bioanalyzer.
Using this library, we performed one full lane sequence on two paired-end 150bp Flow Cells using on an Illumina Nextseq550.

value: Peyer's patch

value: BALB/c


title: CNT IMC Mice M1 with 5TGM1 WT

description: 5TGM1 WT Tumor S1


title: V(D)J in autonomy

city: Oeiras

first: Vera

last: Martins

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

data_processing:
Illumina  sequencer  base  call  files  (BCL)  were  processed  using  Cell  Ranger  mkfastq  pipeline generating FASTQ files for both the 5′ expression library and the V(D)J libraries.
Reads were mapped to the mouse genome build mm10 (available from 10X Genomics).
The 5′ gene-expression libraries were then analyzedwith the Cell Ranger count pipeline v3.0.2.
The Seurat R package (v. 3.1.3.9002)29was used to perform the quality-control, integration, dimensional reduction, clustering and exploration of control and autonomy scRNA-seq data sets.
Genome_build: Mouse genome build mm10 (available from 10X Genomics).
Supplementary_files_format_and_content: Tab-delimited text files with raw gene expression counts obtained with Cell Ranger count pipeline by turnover and autonomy samples.
Supplementary_files_format_and_content: Tab-delimited text files with TCR annotation tables from V(D)J libraries by turnover and autonomy samples.

source_name: thymocyte

growth_protocol: Wild type thymi transplanted for 28 days

extract_protocol:
Thymi were prepared by gently smashing and passing through a 40uM filter to prepare single cell suspensions. Thymocytes were sorted and sequenced using the Chromium Single Cell 5′ Library and the Gel Bead Kit (10x Genomics).
Libraries were constructed using the Chromium Single-Cell 5′ reagent kit, V(D)J Mouse T Cell Enrichment Kit, 5′ Library Construction Kit, and i7 Multiplex Kit (10x Genomics, CA)

tag: condition

value: autonomy

value: DN3-DN4, ISP and double positive thymocytes


title: CA8_E2F1_1

description: small RNA fraction


title: gene expression in autonomy


title: KP_MF

value: tumor bearing mice (KP tumors d30)


title: CA5_NT4_1

description: small RNA fraction

value: transfected with control siRNA


title: CA7_NT4_3

description: small RNA fraction


title: gene expression in turnover

value: turnover


title: lDP autonomy RP1138 all

data_processing:
Quality control using FastQC
Samples  aligned using Hisat2
counts obtained with featureCounts
Sequence alignments’ quality using Qualimap
Differential gene expression analysis using the DESeq2 package in R
Genome_build: mm10 GRCm38
Supplementary_files_format_and_content: Tab-delimited text file with gene expression raw counts obtained with featureCounts
Supplementary_files_format_and_content: Tab-delimited text files with differentially expressed genes identified with DESeq2 R package

extract_protocol:
Thymi were prepared by gently smashing and passing through a 40uM filter to prepare single cell suspensions. DN3 and CD4 CD8 double-positive thymocytes were purified by FACS sort into Qiagen RLT lysis buffer. RNA was separated from genomic DNA using a modified oligo-dT bead-based method.
Libraries were prepared following the Pico Nextera protocol.

value: DP


title: lDP autonomy RP1135 all


title: lDP autonomy RP1136 all


title: lDP autonomy RP1133 all


title: kDP turnover RP1141A all


title: CA6_NT4_2

description: small RNA fraction


title: V(D)J in turnover


title: kDP turnover RP1141B all


title: kDP turnover RP1140A all


title: jDN3 autonomy RP1138 all


title: kDP turnover RP1140B all


title: jDN3 autonomy RP1135 all


title: jDN3 autonomy RP1133 all


title: jDN3 autonomy RP1137 all


title: lDP autonomy RP1137 all


title: jDN3 autonomy RP1134 all


title: iDN3 turnover RP1141B all


title: Mtb + Rapa, 16h, polysome, biological replicate 4

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: polysome RNA

hyb_protocol: Arrays hybridization was performed for 16 hours at 45 °C in a GeneChip Hybridization Oven 640.

scan_protocol: Each array were scanned using the Affymetrix GeneChip Scanner 3000 7G to generate the raw data (.CEL file)

data_processing:
CEL files were first processed with the Affymetrix collection of command line programs Analysis Power Tools (APT, v1.16.0) using the apt-probeset-summarize command in order to estimate the intensity at gene level with the RMA-sketch normalization. R v3.1.2 (www.r-project.org) environment and Bioconductor tRanslatome package was used to find out the probe sets that showed significant (FDR < 0.01) differential expression between experimental conditions.
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.na34.hg19.transcript.csv

source_name: human DC, MTB infected, rapamycin treated, translatome

label_protocol: Each DNA fragment is end-labelled with biotin using terminal deoxynucleotidyltransferase (TdT) (Affymetrix).

growth_protocol: Human peripheral blood mononuclear cells were isolated from buffy coats collected from healthy donors. To generate human primary DC, isolated CD14+ monocytes were cultured with 50 ng/ml GM-CSF and 1000 U/ml IL-4 (R&D Systems) for 5 days at 0.5x10^6 cells/ml in RPMI 1640 (Lonza), supplemented with 2 mM L-glutamine and 15% Fetal Bovine Serum (BioWhittaker). At day 5 the cells were tested for their differentiation status by evaluating CD1a expression (>90% CD1a+) and lack of CD14 (>95% CD14-).

extract_protocol: Total RNA was isolated from 1x10^6 infected or not infected DC, treated or not with rapamycin using Trizol (Invitrogen, Thermo Fisher Scientific) and by following manufacturer’s recommendations. Polysome-associated RNA were prepared as previously described in Livingstone et al, 2015 PMID: 26207988

treatment_protocol: Before infection and/or treatment, cell medium was replaced with RPMI without antibiotics and supplemented with 2 mM L-glutamine and 15% FBS. The deprivation of differentiating cytokines did not affect DC survival rate, which was >90%. DC cultures were then infected with virulent Mycobacterium tuberculosis (Mtb, H37Rv) at multiplicity of infection (MOI) of 1 bacterium/cell for 16 hours. Where indicated, rapamycin was added to not infected and Mtb-infected DC for 12 hours (4 hours after Mtb infection).

value: primary dendrtitic cells

value: MTB infected, rapamycin treated


title: Mtb, 16h, total, biological replicate 4

description: total RNA

source_name: human DC, MTB infected, transcriptome

value: MTB infected


title: iDN3 turnover RP1141A all


title: Mtb + Rapa, 16h, total, biological replicate 4

description: total RNA

source_name: human DC, MTB infected, rapamycin treated, transcriptome


title: Rapamycin, 12h, total, biological replicate 3

description: total RNA

source_name: human DC, rapamycin treated, transcriptome

value: rapamycin


title: Untreated, total, biological replicate 4

description: total RNA

source_name: human DC, untreated, transcriptome

value: untreated


title: Rapamycin, 12h, total, biological replicate 4

description: total RNA


title: iDN3 turnover RP1140B all


title: Mtb + Rapa, 16h, polysome, biological replicate 3

description: polysome RNA


title: Mtb, 16h, polysome, biological replicate 4

description: polysome RNA

source_name: human DC, MTB infected, translatome


title: iDN3 turnover RP1140A all


title: Rapamycin, 12h, polysome, biological replicate 4

description: polysome RNA

source_name: human DC, rapamycin treated, translatome


title: Mtb + Rapa, 16h, total, biological replicate 3

description: total RNA


title: Untreated, total, biological replicate 3

description: total RNA


title: Untreated, polysome, biological replicate 4

description: polysome RNA

source_name: human DC, untreated, translatome


title: Mtb, 16h, polysome, biological replicate 3

description: polysome RNA


title: Rapamycin, 12h, polysome, biological replicate 3

description: polysome RNA


title: KP_MF

data_processing:
For scRNAseq GEX libraries: read-I1_si-***.fastq.gz = cell barcode (14bp) & read-RA_si-***.fastq.gz = transcript (98bp) +UMI (10bp)
Gene expression libraries were aligned to the mm10 reference transcriptome and count matrices were generated using the default Cell Ranger v1 workflow, using the “raw” matrix output.
Genome_build: mm10

tag: strain

tag: group

value: Tumor bearing mice (KP tumors d30)


title: Naive_MF

value: Naive mice


title: MC29TT-pos-1

description: tdTomato positive cells

data_processing:
For scRNAseq GEX libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological.
Gene expression libraries were aligned to the mm10 reference transcriptome and count matrices were generated using the default Cell Ranger 2.1 workflow, using the “raw” matrix output.
Genome_build: mm10
Supplementary_files_format_and_content: .tsv
Supplementary_files_format_and_content: .mtx

extract_protocol:
Single cell suspensions were obtained from lung followed by digestion with collagenase IV 0.25mg/ml (Sigma) at 37°C for 30min followed by passing through a 70mm cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 2min at room temperature.
For each mouse scRNAseq sample, 8,500 monocytes and macrophages were sorted as CD45+LINNEG (CD3/CD19/NKP46) CD11B+LY6GNEG and encapsulated using the 10X Chromium 3’ v2 chemistry kit according to manufacturer instructions. Sequencing libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed by CyberGreen qPCR library quantification assay (KAPA). Samples were sequenced on an Illumina Nextseq 500 using the 75-cycle kit to a depth of 100 million reads per library.


title: MC29TT-neg-2

description: tdTomato negative cells


title: MC29TT-neg-1

description: tdTomato negative cells


title: MC29TT-pos-2

description: tdTomato positive cells


title: MC29NT-pos-1

description: tdTomato positive cells

value: naive Map17CreER-LSL-R26-tdTom


title: MC29NT-neg-1

description: tdTomato negative cells

value: Enriched sorted monocytes and macrophages


title: MC68TP2

description: YFP positive cells


title: Rapamycin, 12h, total, biological replicate 2

description: total RNA


title: MC68TN1

description: YFP negative cells


title: Mtb + Rapa, 16h, total, biological replicate 2

description: total RNA


title: Mtb, 16h, total, biological replicate 3

description: total RNA


title: MC29NT-pos-2

description: tdTomato positive cells


title: Mtb, 16h, total, biological replicate 2

description: total RNA


title: Untreated, total, biological replicate 2

description: total RNA


title: Untreated, polysome, biological replicate 3

description: polysome RNA


title: Mtb + Rapa, 16h, total, biological replicate 1

description: total RNA


title: Mtb + Rapa, 16h, polysome, biological replicate 1

description: polysome RNA


title: Rapamycin, 12h, polysome, biological replicate 2

description: polysome RNA


title: Mtb, 16h, polysome, biological replicate 2

description: polysome RNA


title: Mtb + Rapa, 16h, polysome, biological replicate 2

description: polysome RNA


title: Rapamycin, 12h, polysome, biological replicate 1

description: polysome RNA


title: Untreated, polysome, biological replicate 2

description: polysome RNA


title: Untreated, total, biological replicate 1

description: total RNA


title: MC29NT-neg-2

description: tdTomato negative cells


title: MC68NP1

description: YFP positive cells

value: naive Cx3CR1CreER-LSL-R26-YFP