title: H3K9me2.lin15B.rep1


title: colon_Snap25_cre-neg_ip_SPF_1

status: Public on Aug 13 2020

type: SRA

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
Library strategy: Ribo-Seq
Kallisto alignment
Genome_build: Ensembl Mus musculus release 91: GRCm38.p5 (GCA_000001635.7)

molecule: total RNA

organism: Mus musculus

source_name: Immunoprecipitated ribosome-bound mRNA from colon myenteric plexus of specific pathogen free Snap25:RiboTag Cre-negative mice

extract_protocol: Duodenum, ileum, and colon myenteric plexus was dissected into PBS with cycloheximide (0.2 mg/mL) (PBS/CHX). The RiboTag immunoprecipitation protocol (http://depts.washington.edu/mcklab/RiboTagIPprotocol2014.pdf)  was then followed with the following modifications: All samples were homogenized by hand with a dounce homogenizer in 2.5 mL supplemented homogenization buffer (changes per 2.5 mL: 50 µl Protease Inhibitor, 75 µl heparin (100 mg/mL stock), 25 µl SUPERase In RNase Inhibitor). Samples were then centrifuged for 10 minutes at 10,000 G, after which 800 µl of supernatant was removed and 5µL of anti-HA antibody (Abcam, ab9110) was added. For input samples, 40uL of supernatant was removed and 60uL of PicoPure lysis buffer was added. These input samples were then put at -80°C. Immunoprecipitated samples were kept rotating at 4°C with antibody for 1 hour. 200 µl of Thermo Protein magnetic A/G beads were washed with homogenization buffer, added to the sample, and kept rotating for 30 minutes at 4°C. The beads were washed four times with high-salt buffer and samples were eluted with 100 µl of PicoPure lysis buffer.  RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

tag: strain

tag: tissue

value: Colon myenteric plexus


title: HTZ1.lin35.rep2

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
ChIP-seq reads were aligned to a concatenated ce11+cb3 assembly of the C. elegans and C. briggsae genomes using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm) (Li and Durbin, 2010).
The SAMtools v. 0.1.19 ‘view’ utility (Li et al., 2009) was used to convert the alignments to BAM format. Normalized mapq10 ChIP-seq coverage tracks were generated using the BEADS algorithm (Cheung et al., 2011).
Genome_build: ce11 + cb3 (concatenated)
Supplementary_files_format_and_content: BEADS-normalized genome-wide linear read coverage (from reads with MAPQ value >= 10)

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: HTZ1.lin35.whole worm

growth_protocol: Starved L1 animals were collected by bleaching synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C. Following bleaching, eggs were hatched at 25°C in M9 and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen.

extract_protocol:
Frozen starved L1 worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 10-20 ug of DNA was used per ChIP reaction.
ChIP DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used.

tag: developmental stage

value: starved L1

tag: growth temperature

value: whole worm

tag: chip antibody

tag: sample id


title: PCOS-day12-rep1

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
Day 12-3010-PCOS
Pair-match 1-PCOS

data_processing:
Sequencing reads were trimmed for adapter sequence with Trimmomatic v0.39, and to a max length of 50bp
Trimmed reads were aligned to the human hg19 (GRCh37) reference genome with bowtie2 v2.3.5, specifying the -x 2000 parameter
Alignments were filtered to remove reads mapping to mitochondrial chromosome, reads with mapq score < 30, improperly paired reads as specified by samtools 0x02 flag, and duplicate reads determined by Picard Tools
Peaks were called on each sample with MACS2 v2.1.2 with a significance threshold of p-value < 0.05. Peaks on canonical chromosomes were retained.
Differential analysis of peak regions was performed using DiffBind v2.12.0
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files output from MACS2, contain peak regions surpassing p-value < 0.05 threshold in each sample
Supplementary_files_format_and_content: diffPeak.bed files contain the genomic coordinates of the significant differential peaks (FDR < 0.05) for each comparison

organism: Homo sapiens

source_name: subcutaneous adipose tissue

growth_protocol: Adipose stem cells were plated in 10 cm dish containing DMEM/10% FCS, 0.05 U/ml penicillin, 0.05 mg/ml streptomycin, 1.25 mg/ml fungizone and cultured at 37°C until confluency and expanded for 2 additional generations. Subsequently, generation 4 ASCs were cultured in adipocyte differentiation medium consisting of DMEM/Ham's F-12 (1:1, v/v), HEPES, pH 7.4, fetal bovine serum, biotin, pantothenate, human insulin, dexamethasone, 3-isobutyl-1-methylxanthine (IBMX), PPARg agonist, penicillin, streptomycin, and amphotericin B (Zen-bio) at 37°C for 3-12 days to allow for differentiation into mature adipocytes.

extract_protocol:
At days 0, 3, and 12, cells were trypsinized and 100,000 cells were subject to nuclei preparation for ATAC-Seq.
ATAC-seq libraries were generated according to Berostro et al. (doi: 10.1002/0471142727.mb2129s109) with minor modifications. Nuclei were treated with Tn5 transposon TDE1 (Nextera DNA Library Prep kit, Illumina, San Diego, CA) for 35 min at 37°C. The transposition reaction was then purified using Zymo DCC-5 columns (Zymo Research, Irvine, CA). Following, Polymerase Chain Reaction (PCR) was performed using 25 μl NEBNext High-Fidelity 2x PCR Master Mix (NEB, MA, Boston) 4 µl of each Index 1 (i7) and index 2 (i5) (Nextera XT Index kit, Illumina, San Diego, CA), 2 µl of PPC (Illumina, San Diego, CA) and 15 µl of purified tagmentation reaction. After performing the initial extension and 5 PCR cycles, quantitative PCR was performed on 5 µl of the previous PCR reaction by adding 1 µl of SYBR Green (15x), 1 µl of PPC, 5 μl NEBNext High-Fidelity 2x PCR Master Mix and 3 µl of H2O in a final volume of 15 µl for 20 cycles. The number of additional cycles was determined as the cycle number corresponding to ¼ of maximum fluorescent intensity. Final libraries were purified using 45 µl (1:1 ratio) of SPRI beads (Beckman and Coulter, Indianapolis, Indiana) cat# B23318). Final libraries were visualized on a TapeStation 2200 using a D1000 ScreenTape. Libraries were pooled and paired-end sequenced (PE 2X100) on the Illumina HiSeq4000.

tag: female type

value: Polycystic Ovary Syndrome (PCOS)

value: subcutaneous adipose


title: Ctrl-day12-rep3

description:
Day 12-3004-control
Pair-match 3-control

value: control


title: HTZ1.N2.rep1

source_name: HTZ1.N2.whole worm

value: N2 (Bristol)


title: ileum_Snap25_cre-pos_ip_GF_1

source_name: Immunoprecipitated ribosome-bound mRNA from ileum myenteric plexus of germ free Snap25:RiboTag Cre-positive mice

value: Ileum myenteric plexus


title: ileum_Snap25_cre-pos_ip_GF_5


title: Ctrl-day12-rep2

description:
Day 12-3027-control
Pair-match 2-control


title: HTZ1.lin35.rep1


title: ileum_Snap25_cre-neg_ip_GF_3

source_name: Immunoprecipitated ribosome-bound mRNA from ileum myenteric plexus of germ free Snap25:RiboTag Cre-negative mice


title: HTZ1.N2.rep2


title: ileum_Snap25_cre-pos_ip_GF_2


title: PCOS-day3-rep3

description:
Day 3-3006-PCOS
Pair-match 3-PCOS


title: Ctrl-day12-rep1

description:
Day 12-3036-control
Pair-match 1-control


title: PCOS-day3-rep2

description:
Day 3-3019-PCOS
Pair-match 2-PCOS


title: ileum_Snap25_cre-neg_ip_GF_1


title: ileum_Snap25_cre-neg_ip_GF_2


title: Ctrl-day3-rep3

description:
Day 3-3004-control
Pair-match 3-control


title: ileum_Snap25_cre-pos_ip_SPF_5

source_name: Immunoprecipitated ribosome-bound mRNA from ileum myenteric plexus of specific pathogen free Snap25:RiboTag Cre-positive mice


title: Ctrl-day3-rep2

description:
Day 3-3027-control
Pair-match 2-control


title: ileum_Snap25_cre-pos_ip_SPF_4


title: Batf-/- Batf3-/-  SpDC2_activated (IFNγ+LPS)_rep2

type: RNA

city: Saint Louis

first: Sunkyung

last: Kim

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

description: Batf–/– Batf3–/– SpDC2_activated (IFNγ+LPS)

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: cDC2 isolated from Batf-/- Batf3-/-  spleen

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: Splenic cDC2 sort-purifed from WT or Batf–/– Batf3–/– mice. Some of the purified cDCs were activated by pre-treatment with IFNγ (100 ng/ml) for 1 h and stimulation with E. coli LPS (1 μg/ml) for another 3 h.

value: spleen

tag: genotype

value: Batf-/- Batf3-/-

tag: activation status

value: activated (IFNgamma+LPS)


title: WT_SpDC2_activated (IFNγ+LPS)_rep2

description: WT_SpDC2_activated (IFNγ+LPS)

source_name: cDC2 isolated from WT spleen

value: WT


title: WT_SpDC2_resting_rep1

value: resting


title: WT_SpDC1_resting

source_name: cDC1 isolated from WT spleen


title: WT_SpDC2_activated (IFNγ+LPS)_rep1

description: WT_SpDC2_activated (IFNγ+LPS)


title: PCOS-day3-rep1

description:
Day 3-3010-PCOS
Pair-match 1-PCOS


title: WT_SpDC2_resting_rep2


title: Ctrl-day3-rep1

description:
Day 3-3036-control
Pair-match 1-control


title: PCOS-day0-rep3

description:
Day 0-3006-PCOS
Pair-match 3-PCOS


title: ileum_Snap25_cre-pos_ip_SPF_2


title: ileum_Snap25_cre-pos_ip_SPF_3


title: WT_Flt3L_cDC2_rep1

description: cDC1 from WT BM progenitor

source_name: cDC1 from WT BM progenitor

growth_protocol: Irf4 or Irf8 was retrovirally re-expressed in Irf4–/– Irf8–/– CD117hi BM progenitors at low or high levels and then cultured with Flt3L for 7 days.

treatment_protocol: MHC II+ CD11c+ B220– cDC (Irf4–/– Irf8–/–),  MHC II+ CD11c+ B220– CD24+ CD172– cDC1 (WT), or  MHC II+ CD11c+ B220– CD172+ cDC2 (WT) were sort-purified to extract RNA for microarray analysis.

value: bone marrow

tag: cell type


title: Batf-/- Batf3-/- SpDC2_activated (IFNγ+LPS)_rep1


title: ileum_Snap25_cre-pos_ip_SPF_1


title: WT_Flt3L_cDC2_rep2

description: cDC1 from WT BM progenitor


title: Batf-/- Batf3-/-  SpDC2_resting_rep2

description: Batf–/– Batf3–/– SpDC2_resting


title: Batf-/- Batf3-/-  SpDC2_resting_rep1

description: Batf–/– Batf3–/– SpDC2_resting


title: PCOS-day0-rep2

description:
Day 0-3019-PCOS
Pair-match 2-PCOS


title: WT_Flt3L_cDC1_rep1

description: cDC1 from WT BM progenitor


title: IRF4/8_DKO_Flt3L_cDC_HIGH_IRF8_rep2

description: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF8 at high levels

value: cDC

tag: retroviral expression

value: high IRF8


title: IRF4/8_DKO_Flt3L_cDC_HIGH_IRF4_rep2

description: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF4 at high levels

value: high IRF4


title: IRF4/8_DKO_Flt3L_cDC_LOW_IRF8_rep2

description: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF8 at low levels

value: low IRF8


title: IRF4/8_DKO_Flt3L_cDC_LOW_IRF8_rep1

source_name: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF8 at low levels


title: PCOS-day0-rep1

description:
Day 0-3010-PCOS
Pair-match 1-PCOS


title: IRF4/8_DKO_Flt3L_cDC_HIGH_IRF8_rep1

source_name: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF8 at high levels


title: IRF4/8_DKO_Flt3L_cDC_HIGH_IRF4_rep1

source_name: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF4 at high levels


title: Ctrl-day0-rep3

description:
Day 0-3004-control
Pair-match 3-control


title: IRF4/8_DKO_Flt3L_cDC_LOW_IRF4_rep2

description: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF4 at low levels

value: low IRF4


title: ileum_Snap25_cre-neg_ip_SPF_3

source_name: Immunoprecipitated ribosome-bound mRNA from ileum myenteric plexus of specific pathogen free Snap25:RiboTag Cre-negative mice


title: ileum_Snap25_cre-neg_ip_SPF_2


title: Ctrl-day0-rep2

description:
Day 0-3027-control
Pair-match 2-control


title: ileum_Snap25_cre-neg_ip_SPF_4


title: Ctrl-day0-rep1

description:
Day 0-3036-control
Pair-match 1-control


title: duodenum_Snap25_cre-pos_ip_GF_8

source_name: Immunoprecipitated ribosome-bound mRNA from duodenum myenteric plexus of germ free Snap25:RiboTag Cre-positive mice

value: Duodenum myenteric plexus


title: duodenum_Snap25_cre-pos_ip_GF_6


title: Day7.rep3

city: jingzhou

first: xia

middle: li

last: huang

state: hubei

address: Yangtze university

country: China

institute: Yangtze university

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to mice reference mRNA using the Bowtie1 software
Using R version 3.4.2 software to find differential genes
The web-based program DAVID was used to analyze the function of differentially expressed genes associated with Salmonella infection
InnateDB, was used to identify significantly regulated pathways between different time points.
The significantly enriched gene expression regulators of these differentially expressed gene lists were identified by Gene Expression Regulator Enrichment Analysis
Genome_build: Muscomorpha (taxid:43733)
Supplementary_files_format_and_content: Reads count (tab deli text)

source_name: Peripheral blood

extract_protocol: Sequencing libraries were prepared using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina Inc., USA). Approximately 10 μg of total RNA from each sample was used for library construction and RNA sequencing

value: Peripheral blood

tag: infection

value: Salmonella enterica serovar Typhimurium LT2

tag: timepoint

value: day 7


title: Day7.rep2


title: Day 16 sgMDM4 Rep. 3

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
mRNA-Seq reads were aligned to hg19 and KSHV genomes using STAR-Seq. Raw read counts were generated using HTSeq. Differential gene expression analysis was performed using DESeq2 (KO/KD vs. respective AAVS1 control)
Genome_build: hg19, KSHV (BAC16 reference)
Supplementary_files_format_and_content: FPKM or HTSeq counts

molecule: polyA RNA

growth_protocol: All cells were grown in RPMI-1640 containing 10 µg/mL gentamycin, 0.05 mM β-mercaptoethanol and 20% Serum Plus-II media. Cells were maintained at densities between 2E5 and 1E6 cells/mL

extract_protocol:
Harvested cell pellets were resuspended in 1 mL TRIzol reagent and purified using Direct-zol RNA Miniprep with in-column DNAseI digestion. Total RNA was eluted in 50 µL water.
mRNA-Seq libraries were constructed by the University of Chicago Genomics Facility using the TruSeq RNA Library Prep Kit.

treatment_protocol: Cas9 or dCas9-KRAB cells were infected with lentiviruses expressing sgRNAs against AAVS1, IRF4, BATF, MDM4 or vIRF3.

value: BC-3 Cas9 cells

value: MDM4 KO


title: Day 16 sgMDM4 Rep. 2


title: IRF4/8_DKO_Flt3L_cDC_LOW_IRF4_rep1

source_name: cDC from Irf4–/– Irf8–/–  BM progenitors retrovirally expressing IRF4 at low levels


title: Day7.rep1


title: Day2.rep3

value: day 2


title: Day2.rep4


title: WT_Flt3L_cDC1_rep2

description: cDC1 from WT BM progenitor


title: Day 16 sgMDM4 Rep. 1


title: duodenum_Snap25_cre-pos_ip_GF_5


title: Skin WT rep2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from skin

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.3.1).

source_name: Skin from WT mice

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

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

treatment_protocol: No treatment was applied to the animals

value: Whole skin


title: Skin Vav2(Onc) rep3

description: Gene expression data from skin

source_name: Skin from Vav2(Onc) mice


title: Day2.rep2


title: Skin WT rep1

description: Gene expression data from skin


title: Skin Vav2(Onc) rep1

description: Gene expression data from skin


title: Skin Vav2(Onc) rep2

description: Gene expression data from skin


title: Day 16 sgAAVS1 Rep. 3


title: Day2.rep1


title: duodenum_Snap25_cre-neg_ip_GF_3

source_name: Immunoprecipitated ribosome-bound mRNA from duodenum myenteric plexus of germ free Snap25:RiboTag Cre-negative mice


title: Skin WT rep3

description: Gene expression data from skin


title: duodenum_Snap25_cre-neg_ip_GF_2


title: Day7.rep4


title: Day0.rep4

value: day 0


title: duodenum_Snap25_cre-neg_ip_GF_1


title: Day0.rep3


title: Day 16 sgAAVS1 Rep. 2

value: WT


title: Day0.rep1


title: duodenum_Snap25_cre-pos_ip_SPF_6

source_name: Immunoprecipitated ribosome-bound mRNA from duodenum myenteric plexus of specific pathogen free Snap25:RiboTag Cre-positive mice


title: SLC4A11 KD 3

city: Los Angeles

first: Wenlin

last: Zhang

state: CA

address: 200 Stein Plaza, Dserc 3-143

institute: UCLA, Jules Stein Eye Institute

description:
SLC4A11 KD
255_S6_R1_001
255_S6_R2_001

data_processing:
Alignment - HISAT2, --no-unal --no-discordant --no-mixed
Assemble and Quantify - STRINGTIE
DGE analysis - LIMMA and VOOM
Genome_build: GRCh38
Supplementary_files_format_and_content: txt - list of DGE

source_name: corneal endothelium

growth_protocol: Primary cultures of human corneal endothelial cells (pHCEnC) were isolated from donor corneas as previously described (Frausto, et al. 2016). Cells were plated in laminin coated cell culture plastic and cultured in a 1:1 mixture of F12-Ham’s and M199 (F99) medium. Experiments were performed when the cells achieved an intact and confluent monolayer.

extract_protocol:
Total RNA from cultured pHCEnC was isolated in TRI Reagent and purified with the RNeasy Clean-Up Kit (Qiagen).
Purified total RNA from pHCEnC was prepared for RNA-seq libraries using KAPA mRNA HyperPrep Kit.

treatment_protocol: Confluent pHCEnC were transfected with 10nM anti-SLC4A11 siRNA (siRNA-CrCrGrArArArGrUrArCrCrUrGrArArGrUrUrArArArGrArACT) or scrambled siRNA (OriGene Technologies) using Lipofectamine LTX (Life Technologies). At 72 hrs post-transfection, the cells were lysed for RNA isolation.

value: primary cultured human corneal endothelial cells

tag: passage

tag: treatment

value: SLC4A11 siRNA knock-down


title: Day 16 sgAAVS1 Rep. 1


title: H3K27me3_ChIP-seq_E35A-H2B_2_Input

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Input DNA from 3T3-L1 cells ectopically expressing E35A mutant histone H2B

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to (1) “bed” files for later Metagene and read-density analyses and (2) “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: 3T3-L1 cells were obtained from the American Type Cell Culture (ATCC, CL-173) and were regularly verified as mycoplasma-free.  They were cultured in DMEM (Cellgro, 10-017-CM) supplemented with 10% fetal bovine serum (Sigma, F8067) and 1% penicillin/streptomycin.

extract_protocol:
3T3-L1  cells were seeded at ~3 x 106 cells per 15 cm diameter plate and treated as described above.  The cells were cross-linked with 1% paraformaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  The cells were then collected and lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail).  A crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.9, 1 mM DTT, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail), and incubated on ice for 10 minutes.  The chromatin was sheared at 4°C by sonication using a Bioruptor UC200 at the high setting for thirteen cycles of 30 seconds on and 30 seconds off to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl, pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail) and pre-cleared with protein A Dynabeads.  The pre-cleared supernatant was used in immunoprecipitation reactions with antibodies against the factor of interest or with rabbit IgG as a control, and incubated overnignt at 4°C. The protein A Dynabeads was then added and incubated at 4°C for 2 hours. The immunoprecipitated material was washed once with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail), once with high-salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail), once with LiCl wash buffer (10 mM Tris-HCl, pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1x phosphatase inhibitor cocktail, and 1x complete protease inhibitor cocktail), and once with 1x Tris-EDTA (TE).  The immunoprecipitated material was eluted in elution buffer (100 mM NaHCO3, 1% SDS) and was then digested with proteinase K and RNase H to remove protein and RNA, respectively.  The immunoprecipitated genomic DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. .
After purification, 10 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: For H2B-Ser36p ChIP-seq, 3T3-L1 cells were cultured in 15 cm  dishes, and treated with or without 10 uM of BYK204165 for 2 hours before collection. For H3K27me3 ChIP-seq, 3T3-L1 cells expressing FLAG-tagged wild-type or mutant (E35A) histone H2B were seeded in 15 cm  dishes.

value: mouse fibroblasts

tag: sample type


title: H3K27me3_ChIP-seq_E35A-H2B_Input


title: H3K27me3_ChIP-seq_WT-H2B_1_Input

description: Input DNA from 3T3-L1 cells ectopically expressing WT histone H2B


title: SLC4A11 KD 2

description:
SLC4A11 KD
254_S5_R1_001
254_S5_R2_001


title: duodenum_Snap25_cre-pos_ip_SPF_4


title: H3K27me3_ChIP-seq_WT-H2B_2

description: ChIP-enriched DNA from 3T3-L1 cells ectopically expressing WT histone H2B


title: scRNA 3

description:
scRNA
246_S3_R1_001
246_S3_R2_001

value: scrambled RNA


title: duodenum_Snap25_cre-neg_ip_SPF_4

source_name: Immunoprecipitated ribosome-bound mRNA from duodenum myenteric plexus of specific pathogen free Snap25:RiboTag Cre-negative mice


title: duodenum_Snap25_cre-neg_ip_SPF_1


title: scRNA 2

description:
scRNA
245_S2_R1_001
245_S2_R2_001


title: H3K27me3_ChIP-seq_WT-H2B_1


title: scRNA 1

description:
scRNA
244_S1_R1_001
244_S1_R2_001


title: Day0.rep2


title: Duod_1

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
barcode and adapter removal: FASTX toolkit (v0.0.14)
quality filtering: FastQC (v0.11.8): quality >20, leading/trailing 5, minlength 36
remove non-mRNAs: Bowtie2: rRNA, miRNA, tRNA, piRNA, snRNA, rmsk removal
RSEM: RSEM (v1.3.1): strand-specific, bowtie2, genome-bam
DESeq2: DESeq2(1.26.0):
Differential Expression Analysis: DEBrowser  1.14.2: To perform DE analysis DEBrowser interface used
RNA-Seq pipeline : DolphinNext 1.1.12: To execute data processing steps above for all the samples
Genome_build: mm10
Supplementary_files_format_and_content: countMatrix.tsv:RSEM expected counts; deResults.tsv: DeSeq2 L2FC & adjusted p-values for comparisons. The read counts in this table are MRN normalized using deBrowser.

source_name: intestinal epithelial cells

extract_protocol:
Total RNAs were extracted using Rneasy Micro kit (Qiagen)
Libraries were constructed using Illumina Truseq RNA sample preparation kit.
Sequencing was run on an Illumina HiSeq2000 instrument using multiplexed 50 bp single-end reads.

value: intestinal epithelial cells

value: Wild type


title: Ngn3addon_2

value: Mixed C57BL6 and CD1


title: Ngn3EGFP_2


title: vIRF3 i8 Rep. 3

value: BC-3 dCas9-KRAB cells

value: VIRF3 KD


title: H3K27me3_ChIP-seq_WT-H2B_2_Input


title: Ngn3addon_1


title: Ngn3EGFP_1


title: FB77_G4_inp

city: Milwaukee

first: Michele

middle: A

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

description: Input

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2.
Peaks were called using MACS2 at q value 0.05.
Peaks were annotated using annotatePeaks.pl script in Homer.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph and xlsx

source_name: Stomach mucosa

growth_protocol: Adult mature mice 10-12 months old were euthanized and stomachs were chopped into 7-8 pieces and incubated 30 mins in BSS solution at vigorous vortexing.

extract_protocol:
Lysates were clarified from sheared nucleic DNA and histone-DNA complexes or GATA4-DNA complexes were isolated with antibody or streptavidin beads.
Libraries were prepared according to NEB instructions accompanying the NebNext Ultra II DNA Library Prep Kit for Illumina (Part#7645).

value: G4fb/fb R26 Bira/Bira

tag: age

value: Adult (10-12 months)

value: Stomach


title: duodenum_Snap25_cre-pos_ip_SPF_5

tag: strain

value: Duodenum myenteric plexus


title: RNA-seq_WT-6d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing Wt histone H2B at differentiation day 6

data_processing:
The raw data were subjected to QC analyses using the FastQC tool.  The reads were then mapped to mouse genome (mm10) using the spliced reader aligner TopHat version 2.0.13.  Transcriptome assembly was performed using cufflinks v.2.2.1 with default parameters48.  The transcripts were merged into two distinct, non-overlapping sets using cuffmerge, followed by cuffdiff to call the differentially regulated transcripts.  The significantly (p <0.05) regulated genes from cells expressing the H2B mutants S36A or E35A were compared to wild-type at the indicated time points.
Supplementary_files_format_and_content: Gene-level differential expression file

extract_protocol:
3T3-L1 cells were collected at the indicated time points and total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously.  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000

treatment_protocol: 3T3-L1 cells expressing inducible FLAG-tagged wild-type or mutant (E35A, S36A) histone H2B were seeded in 6-well plates.  Differentiation from preadipocytes into adipocytes was induced in contact-inhibited cells by the addition of MDI cocktail [0.25 mM IBMX (3-isobutyl-1-methylxanthine; Calbiochem, 410957), 1 mM dexamethasone (Sigma, D4902), and 10 mg/mL insulin (Sigma, I-5500)].  The cells were treated with MDI cocktail for 2 days and then cultured in medium containing 10 mg/mL insulin for the indicated time points before collection.

tag: histone

value: WT histone

tag: time point

value: differentiation day 6

tag: cell line


title: FB76_G4_rep2

tag: tissue

tag: chip antibody

value: FlagBio GATA4 purified using streptavidin beads (Invitrogen 11206D, lot 153208730)


title: H3K27me3_ChIP-seq_E35A-H2B_2

description: ChIP-enriched DNA from 3T3-L1 cells ectopically expressing E35A mutant histone H2B


title: vIRF3 i8 Rep. 2


title: duodenum_Snap25_cre-neg_ip_SPF_6


title: SLC4A11 KD 1

description:
SLC4A11 KD
253_S4_R1_001
253_S4_R2_001


title: FB77_G4_rep1


title: RNA-seq_WT-6d-Rep1


title: H3K27me3_ChIP-seq_E35A-H2B_1


title: RNA-seq_WT-4d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing Wt histone H2B at differentiation day 4

value: differentiation day 4


title: RNA-seq_WT-4d-Rep1


title: Duod_2


title: vIRF3 i8 Rep. 1


title: RNA-seq_WT-2d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing Wt histone H2B at differentiation day 2

value: differentiation day 2


title: RNA-seq_WT-0d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing Wt histone H2B at differentiation day 0

value: differentiation day 0


title: B cells untreated 48hr 1

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
RNA-seq: The single-end 75bp were demultiplexed using CASAVAv1.8.2 and Cutadapt (v1.9) was used for read trimming.
RNA-seq: The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
RNA-seq: FeatureCounts was used for read counting after which differential gene expression analysis was performed using Voom-LIMMA packages.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample
ChIP-seq: 20 million single-end 75bp reads were generated per sample. CASAVA (v1.8.2) was used for demultiplexing.
ChIP-seq: The FASTQ files generated were aligned to the mouse reference genome (mm10) using bowtie (v2.2.3).
ChIP-seq: Samtools (v1.3) was used for manipulation of SAM and BAM files and MACS (V2.0.10) was used for peak calling.
ChIP-seq: BigWig file generated using deepTools 2.0
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file generated using deepTools 2.0

source_name: Purified Primary B cells

growth_protocol: B cells were purified from C57Bl/6

extract_protocol:
RNA-seq: RNA was extracted using Qiagen RNeasy Mini kit and gDNA was removed using Qiagen RNAse-Free DNAse set.
RNA-seq: 3’mRNA-sequencing libraries were prepared from 100ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturers instructions and sequenced on the NextSeq 500 (Illumina).
ChIP-seq: Lysates were clarified from sonicated nuclei and Brd4-DNA or H3K27ac-DNA complexes were isolated with antibody. DNA product was purified using Zymo ChIP DNA Clean and Concetrator Kit.
ChIP-seq: ChIP-enriched DNA was processed and sequenced using NEBnext Ultra II kit according to manufacturer’s instructions on Nextseq500 (Illumina).

treatment_protocol: Cells were cultured with LPS (15ug/mL) and were either untreated or treated with JQ1 (250nM). Samples were harvested at indicated hours (2hr, 8hr 48hr for RNA and 2hr, 8hr for ChIP)

tag: cell type and stimulation

value: B cells stimulated with LPS

value: untreated


title: vIRF3 i7 Rep. 3

tag: genotype


title: B cells untreated 48hr 2


title: vIRF3 i7 Rep. 2


title: RNA-seq_WT-0d-Rep2

value: mouse fibroblasts


title: vIRF3 i7 Rep. 1


title: RNA-seq_S36A-6d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing S36A histone H2B at differentiation day 6

value: S36A histone


title: B cells JQ1 48hr 3

value: JQ1 treated


title: RNA-seq_S36A-6d-Rep2


title: iAAVS1 Rep. 3

value: BC-3 dCas9-KRAB cells

value: WT


title: RNA-seq_S36A-4d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing S36A histone H2B at differentiation day 4


title: B cells JQ1 48hr 2


title: RNA-seq_S36A-2d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing S36A histone H2B at differentiation day 2


title: B cells untreated 48hr 3


title: RNA-seq_S36A-2d-Rep1


title: iAAVS1 Rep. 2


title: B cells JQ1 48hr 1


title: RNA-seq_S36A-0d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing S36A histone H2B at differentiation day 0


title: B cells untreated 8hr 3


title: RNA-seq_WT-2d-Rep2


title: iAAVS1 Rep. 1


title: RNA-seq_E35A-6d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing E35A histone H2B at differentiation day 6

value: E35A histone


title: B cells untreated 8hr 2


title: RNA-seq_S36A-0d-Rep1


title: RNA-seq_E35A-6d-Rep2


title: RNA-seq_E35A-4d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing E35A histone H2B at differentiation day 4


title: RNA-seq_E35A-2d-Rep1

description: RNA-seq in 3T3-L1 cells ectopically expressing E35A histone H2B at differentiation day 2


title: RNA-seq_E35A-0d-Rep2

description: RNA-seq in 3T3-L1 cells ectopically expressing E35A histone H2B at differentiation day 0


title: B cells JQ1 8hr 3


title: Day 8 sgBATF Rep. 2

value: BC-3 Cas9 cells

value: BATF KO


title: Day 8 sgAAVS1 Rep. 3


title: B cells untreated 8hr 1


title: Day 8 sgBATF Rep. 1


title: B cells JQ1 8hr 2


title: RNA-seq_E35A-2d-Rep2


title: RNA-seq_E35A-0d-Rep1


title: RNA-seq_S36A-4d-Rep1


title: Day 8 sgAAVS1 Rep. 2


title: Day 8 sgAAVS1 Rep. 1


title: RNA-seq_E35A-4d-Rep2


title: B cells JQ1 8hr 1


title: B cells untreated 2hr 3


title: Day 8 sgBATF Rep. 3


title: B cells untreated 2hr 2


title: Day 3 sgBATF Rep. 3


title: Day 3 sgBATF Rep. 2


title: B cells untreated 2hr 1


title: Day 3 sgBATF Rep. 1


title: B cells JQ1 2hr 2


title: Day 3 sgIRF4 Rep. 2

value: IRF4 KO


title: Day 3 sgIRF4 Rep. 1


title: B cells untreated 0hr 3


title: Day 3 sgAAVS1 Rep. 3


title: B cells untreated 0hr 2


title: Day 3 sgAAVS1 Rep. 2


title: Day 3 sgIRF4 Rep. 3


title: B cells JQ1 2hr 3


title: 9462064012_I

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data were normalized and analyzed using R program, lumi and limma packages.

source_name: SW480 mock2 vehicle 24h -3

label_protocol: cRNA were prepared and labeled with Cy3 dye using Illumina TotalPrep-96RNA Amplification Kit and Illumina Whole-Genome Gene Expression Direct Hybridisation Kit

extract_protocol: RNA was extracted using EZNA Total RNA Kit I, from Omega

treatment_protocol: Cells were treated with either vehicle or 10ng/mL TNFa for either 2 or 24 hours before RNA extraction

tag: colon cancer cell line

value: vehicle 24 hours


title: 9462064012_H

description: replicate 3

source_name: SW480 ERb2 TNFa 2h -3

value: SW480 with stably expressed Erbeta gene

value: 10ng/mL TNFa 2 hours


title: 9462064012_J

description: replicate 3

source_name: SW480 mock2 TNFa 24h -3

value: 10ng/mL TNFa 24 hours


title: 9462064009_L

description: replicate 2

source_name: SW480 ERb2 TNFa 2h -2


title: 9462064012_G

description: replicate 3

source_name: SW480 ERb2 vehicle 2h -3

value: vehicle 2 hours


title: 9462064012_E

description: replicate 3

source_name: SW480 mock2 vehicle 2h -3


title: 9462064012_K

description: replicate 3

source_name: SW480 ERb2 vehicle 24h -3


title: 9462064012_D

description: replicate 2

source_name: SW480 ERb2 TNFa 24h -2


title: 9462064009_D

description: replicate 1

source_name: SW480 ERb2 TNFa 2h -1


title: Day 3 sgAAVS1 Rep. 1

tag: cell type


title: 9462064012_A

description: replicate 2

source_name: SW480 mock2 vehicle 24h -2


title: 9462064012_F

description: replicate 3

source_name: SW480 mock2 TNFa 2h -3


title: 9462064009_K

description: replicate 2

source_name: SW480 ERb2 vehicle 2h -2


title: 9462064009_E

description: replicate 1

source_name: SW480 mock2 vehicle 24h -1


title: 9462064012_L

description: replicate 3

source_name: SW480 ERb2 TNFa 24h -3


title: 9462064009_F

description: replicate 1

source_name: SW480 mock2 TNFa 24h -1


title: 9462064009_H

description: replicate 1

source_name: SW480 ERb2 TNFa 24h -1


title: 9462064009_J

description: replicate 2

source_name: SW480 mock2 TNFa 2h -2


title: 9462064012_C

description: replicate 2

source_name: SW480 ERb2 vehicle 24h -2


title: B cells 8hr Input DNA-2

source_name: Purified Primary B cells


title: 9462064009_C

description: replicate 1

source_name: SW480 ERb2 vehicle 2h -1


title: 9462064012_B

description: replicate 2

source_name: SW480 mock2 TNFa 24h -2


title: 9462064009_G

description: replicate 1

source_name: SW480 ERb2 vehicle 24h -1


title: B cells 8hr JQ1 Brd4 ChIP-2


title: NFKB1/p50_HA-p50 2KR_ChIPSeq

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were trimmed with Trimmomatic (version 0.38) to remove low quality reads.
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie version 2.3.4.3 with default configurations.
Peaks were called using Homer pipeline version 4.10 with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file

growth_protocol: HEK293T cell line was maintained in DMEM supplemented with 10% FBS and 1%PS.

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor/DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (Part# E7103). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer HiSeq4000 following the manufacturer's protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min, and neuralized with Glycine for 5 min at room temperature.

value: HA-tagged p50 2KR muttant (K354R and K356R) expression.

value: Anti-HA tag antibody - ChIP Grade (Abcam, #ab9110)


title: B cells 8hr Unt Brd4 ChIP-2

value: B cells stimulated with LPS

value: untreated


title: NFKB1/p50_HA-p50 WT_ChIPSeq

value: HA-tagged wild type p50 expression.


title: WT_NPFicoll1

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw data was demultiplexed into cells and the data mapped to the mouse mm10 genome build using CellRanger v2.1.1.
Biological replicates for WT-LPS and WT-NPFicoll stimulated B cells were aggregated using the CellRanger aggr function with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: UMI transcript counts for each cell (columns) and all detected genes (rows)

source_name: B cell

extract_protocol:
Adoptively transferred cells were FACS isolated and resuspended in 1xPBS at 1000 cells/ul for GEM loading.
GEM creation and library preparation was performed according to the 10x recommended protocol.

treatment_protocol: B cells of the indicated genotype were harvested from the spleen 72 hours following LPS or NP-Ficoll innoculation.

tag: Sex

value: female

tag: sorting markers

value: Spleen

tag: stimulation

value: NP-Ficoll


title: B cells untreated 0hr 1


title: WT_NPFicoll2


title: WT_LPS2

value: LPS


title: NFKB1/p50_Tamoxifen_ChIPSeq

value: stable TopBP1-ER expression was treated with 500nM tamoxifen for 4 hours.

value: NFKB1/p50 (Santa Cruz, sc-7178X)


title: B cells 8hr Input DNA-1


title: WT_LPS1


title: NFKB1/p50_Vehicle_ChIPSeq

value: stable TopBP1-ER expression was treated with vehicle for 4 hours.


title: B cells 8hr JQ1 Brd4 ChIP-1

value: JQ1 treated


title: 9462064009_A

description: replicate 1

source_name: SW480 mock2 vehicle 2h -1


title: NFKB1/p50_S_ChIPSeq

value: synchronized with double thymidine block and released into S phase in normal medium.


title: B cells 8hr Unt Brd4 ChIP-1


title: NFKB1/p50_G1_ChIPSeq

value: synchronized with double thymidine block and released into normal medium.


title: Input DNA


title: Germination of nrpe1-11 in MS, rep2

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

description: Bisulfite treated DNA

data_processing:
Reads were adapter trimmed using TrimGalore v 0.4.1
Reads were aligned to TAIR10 genome using Bismark v. 0.16.1, no mismateches were allowed
Reads mapped to one position were kept and regions with at least 10 reads were taken for downstream analyses
Methylation and DMR identification was done using methylKit R package
Genome_build: TAIR 10
Supplementary_files_format_and_content: processed files are formatted for methylKit input in .txt.gz

organism: Arabidopsis thaliana

source_name: Germinating seeds

growth_protocol: Seeds were sown in MS media and germinated under 16/8 light/dark photoperiod at 21ºC and 100uE of light intensity

extract_protocol:
DNA was extracted using the DNEasy Plant DNA isolation kit (#69106)
Librariues were generated using the Zymo pico methylKit

treatment_protocol: MS 1X was used as control medium while for salinity we added 100 mM of NaCl to MS

tag: developmental stage

value: Germinating seeds

value: Control

value: PolV


title: Germination of nrpe1-11 in NaCl, rep2

description: Bisulfite treated DNA

tag: treatment

value: Salinity


title: Germination of nrpe1-11 in MS, rep1

description: Bisulfite treated DNA


title: 9345344075_I

description: replicate 3

source_name: HT29 mock2 vehicle 24h -3

value: vehicle 24 hours


title: 9345344075_K

description: replicate 3

source_name: HT29 ERb2 vehicle 24h -3

value: HT29 with stably expressed Erbeta gene


title: Macrophages Nucleus WT

city: Schlieren

first: Marc

last: Pfefferle

state: Schweiz

address: Wagistrasse 12

country: Switzerland

institute: University hospital Zürich (USZ)

data_processing:
Data was then processed using the using CellRanger ATAC software suite (v1.2.0) from 10x genomics. BCL files from each individual sample were demultiplexed using cellranger-atac mkfastq. Read filtering, alignement, barcode counting was done using cellranger atac count and cellranger-atac aggr was used to merge the two samples.
The two filtered digital expression matrices were then merged into one using CellRanger Aggr and then further analyzed using R (v3.6.1) [https://www.R-project.org/].
Supplementary_files_format_and_content: First processed data file is the filtered matrix obtained after CellRanger-ATAC and CellRanger-ATAC Aggr containing peak fragments for every region in each barcoded cell.
Data was further processed in R using the seurat package Signac (v0.2.4). Quality control was assured using a serie of per-cell metrics from the output of CellRanger: total number of fragments per peaks (>3000, <20’000), fraction of fragments in peaks (>15%), ratio reads in blacklist sites according to the ENCODE project (<5%) and nucleosome banding pattern (<10%) as well as transcription start site (TSS) enrichment scores according to ENCODE project (>2) computed using the TSSEnrichement() function of Signac. Normalization was done with a term frequency-inverse document frequency (TF-IDF) normalization using the RunTFIDF() function. Dimensional reduction was performed using singular value decomposition (SVD) on the TD-IDF normalized matrix with the runSVD() function using all features (no previous feature selection step).
UMAP non-linear dimension reduction was performed using RunUMAP() function and clustering with FindNeighbors() and Finclusters() functions with the SLM algorithm. A pseudo-gene expression matrix was created using the FeatureMatrix() function by counting the number of fragments for each cell that map to gene encoding regions of the mouse genome from EnsembleDB including the 2kb upstream region from them. This includes the gene coding region as well as the promoter region whose accessibility can be interpreted as correlated to gene expression. Cell types for each clusters were determined using this pseudo-gene expression matrix. Differentially accessible peaks between Kupffer cells and erythrophagocytes was performed using the FindMarkers() function on the peak region fragment matrix.  Peak coordinates were mapped to genes using the Closestfeature() function with EnsDb.Mmusculus.v79. Motif enrichment analysis was performed using the Findmotifs() function on the differentially accessible peaks with a list of motif position frequency matrices from the JASPAR 2018 database. MotifPlot() function was then used to generate the plots of the position weight matrices for the top overrepresented motifs.
Supplementary_files_format_and_content: Second processed data file is an .rds file containing Seurat class object of the data after quality control, normalization, dimensionality reduction, clustering, motif enrichement analysis
Genome_build: Ensembl GRCm38.p5 Release 91

source_name: Non-parenchymal liver cells enriched for F4/80 positive macrophages

growth_protocol: 8-10 week old male mice

extract_protocol:
The abdominal cavity of a living, deeply anesthetized mouse was opened, and the portal vein was catheterized for in situ liver perfusion and digestion with 50 ml of 0.06 U/ml collagenase B buffered solution (Roche, 11088815001). Once digested, livers were dissected out and the mouse was sacrificed. The digested livers were then mechanically disaggregated in a petri dish on ice and filtered through a 100 μm pore cell strainer. The cell suspensions were centrifuged twice at 60 x g for 2 min at 4°C, and the pellets were discarded. The supernatants were then centrifuged at 300 x g for 5 min at 4°C to obtain a pellet of nonparenchymal liver cells containing liver macrophages. To select for F4/80+ macrophages from liver cell suspensions, Dynabeads Sheep anti-Rat IgG (Invitrogen, 11035), in combination with purified rat anti-mouse F4/80 antibody (BD Pharmingen, 0.5 mg/ml, 565409) ), and a DynaMag™-2 Magnet (Thermo Fisher Scientific, 12321D) were used according to the manufacturer's protocol (Invitrogen). The purity of the separated cells was tested by detecting F4/80 positive cells by FACS. Nuclei were isolated using the Nuclei Isolation for Single Cell ATAC sequencing (10x genomics) protocol, counted and loaded in the chromium controller with a target recovery of 8’000 nuclei.
They were then processed according to the chromium next GEM single Cell ATAC reagent Kits v1.1 protocol. Libraries were pooled equimolarly and sequenced using a NextSeq 500 system according to 10x genomics recommendation. Sequencing depth of 25’000 read pairs per nucleus (paired-end, dual indexing). Read 1N: 50 cycles, i7 Index: 8 cycles, i5 Index: 16 cycles, Read 2N: 50 cycles.

treatment_protocol: No treatment

value: Liver

tag: genotype/variation

value: Spta wt/wt


title: Macrophages Nucleus SPTA

value: Spta sph/sph


title: 9345344075_L

description: replicate 3

source_name: HT29 ERb2 TNFa 24h -3

value: 10ng/mL TNFa 24 hours


title: Germination of nrpe1-11 in NaCl, rep1

description: Bisulfite treated DNA


title: B cells 2hr Unt Brd4 ChIP

value: B cells stimulated with LPS

value: untreated


title: B cells 2hr JQ1 Brd4 ChIP


title: 9345344075_J

description: replicate 3

source_name: HT29 mock2 TNFa 24h -3


title: 9345344075_H

description: replicate 3

source_name: HT29 ERb2 TNFa 2h -3

value: 10ng/mL TNFa 2 hours


title: B cells 2hr Unt H3K27ac ChIP

value: Abcam H3K27ac (ab4729)


title: 9345344075_G

description: replicate 3

source_name: HT29 ERb2 vehicle 2h -3

value: vehicle 2 hours


title: translome_KO2

city: La Jolla

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

description:
riboTag-labeled RNAs
riboRNA_counts.txt

data_processing:
For scRNAseq, reads undergo de-multiplexing and FastQ file generation, CellRanger based mapping and filtering, Seurat R package for QC filtering and normalization, Seurat and monocle for clustering and trajectory
For RNAseq and translome analysis, we performed alignment using STAR (2.5.2b). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. DEGs were analyzed using DeSeq2.
Genome_build: For scRNAseq, mm10. For both RNAseq and translome, Mus musculus, release-90, Ensembl genome (GRCm38)
Supplementary_files_format_and_content: For scRNAseq, Matrix of genes, counts and cell barcodes. For both RNAseq and translome, featurecounts

source_name: purified mOSNs riboTag-labeled RNAs

extract_protocol:
Olfactory epithelium was dissociated to generate the single cell suspension. After removing dead cells, cells were diluted for loading on Chromium chip for 10X Genomics library preparation and subsequent sequencing. For RNAseq, olfactory epithelium single cell suspension was incubated with propidium iodide (final concentration of 1 μg/ml) and OMP-eYFP+ cells were sorted by flow-cytometry. For translome, RiboTag mice bred with mOSN-specific (Omp-Cre) mice, and RiboTag labeled mOSN mRNA was isolated.
Chromium Single Cell Kit [v2 chemistry]. For both RNAseq and translome, libraries were prepared for sequencing using standard Illumina protocols.

value: olfactory epithelium


title: translome_KO3

description:
riboTag-labeled RNAs
riboRNA_counts.txt


title: translome_KO1

description:
riboTag-labeled RNAs
riboRNA_counts.txt


title: B cells 2hr Input DNA


title: 9345344075_F

description: replicate 3

source_name: HT29 mock2 TNFa 2h -3


title: B cells 2hr JQ1 H3K27ac ChIP

value: JQ1 treated


title: translome_WT3

description:
riboTag-labeled RNAs
riboRNA_counts.txt

value: wild type


title: 9345344075_E

description: replicate 3

source_name: HT29 mock2 vehicle 2h -3


title: WT2_H2B input

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

description: WT2 MEF

data_processing:
macs2 callpeak -n SHORTNAME sn --bdg --nomodel --extsize 150 -t SAMPLENAME.bam -c INPUTNAME.bam ; macs2 bdgcmp -t SHORTNAME_treat_pileup.bdg -c SHORTNAME_control_lambda.bdg -m qpois -o SHORTNAME_qvalue.bdg ; cat SHORTNAME_treat_pileup.bdg | sort -k1,1 -k2,2n > tmp.SHORTNAME.bdg; bedGraphToBigWig tmp.SHORTNAME.bdg mm9.chrsizefile SHORTNAME.bw
custom program used to get sum of base coverages from wig file
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated

source_name: murine embryonic fibroblast

growth_protocol: WT (Hells+/-) and KO (Hells-/-) MEF cell lines were grown in high-glucose DMEM (Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Omega Scientific), 1x GlutaMAXTM (Gibco), and 50 U/ml Pen/Strep (Gibco).

extract_protocol:
Lysates were clarified from Mnase digestied nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were constructed from DNA samples (ChIP DNA and Input) with the Illumina TruSeq V3 library construction protocol (Illumina). Sequencing runs were performed on an Illumina NextSeq 500 with 75-base-pair (bp) single-end mode using NextSeq V4 chemistry (flowcells H0Y1PBGXX, H11P6BGXX, and H13V2BGXX)

value: murine embryonic fibroblast

tag: passages

value: SV40 transformed

value: Lsh+/+


title: WT3_H2B

description: WT3 MEF

tag: strain

value: H2B (abcam, ab1790)


title: WT3_H2B input

description: WT3 MEF


title: naïve_3

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

data_processing:
FastQC
Mapping with HISAT2
HTseq-count
DEseq2
Genome_build: Ensembl GRCm38.97
Supplementary_files_format_and_content: tabular format, read counts per gene.

source_name: Mouse splenic CD4+ T cells

growth_protocol: Ex-vivo spleen cells were suspended in complete RPMI1640 medium (Biological Industries, Beit Haemek, Israel) supplemented with 10% FBS, 2 mM L-glutamine, 1.35 g/l sodium bicarbonate, 5 mM HEPES, 50 μM β-mercaptoethanol, 100 μg/ml streptomycin and 100 IU penicillin (Millipore Sigma, Merck KGaA, Germany) in 6 well plates coated with anti-CD3 and anti-CD28.

extract_protocol:
RNA isolation protocol using TRIzol reagent as recommended.
TruSeq RNA Sample Prep Kit v2 (Ilumina, San Diego) according to the kit protocol

treatment_protocol: The plates were incubated in either an incubator set at 37ºC or in an incubator set at 39ºC for 3 hours.

value: Untreated


title: translome_WT2

description:
riboTag-labeled RNAs
riboRNA_counts.txt


title: naïve_2


title: WT1_H2B input

description: WT1 MEF


title: translome_WT1

description:
riboTag-labeled RNAs
riboRNA_counts.txt


title: 9345344071_L

description: replicate 2

source_name: HT29 ERb2 TNFa 2h -2

value: HT29 with stably expressed Erbeta gene


title: RNAseq_KO4

description:
total RNA
RNA_counts.txt

source_name: purified mOSNs


title: 9345344075_B

description: replicate 2

source_name: HT29 mock2 TNFa 24h -2


title: 9345344075_C

description: replicate 2

source_name: HT29 ERb2 vehicle 24h -2

value: vehicle 24 hours


title: WT2_H2B

description: WT2 MEF


title: 39_3

value: Activated at 39 C


title: 9345344075_D

description: replicate 2

source_name: HT29 ERb2 TNFa 24h -2

value: 10ng/mL TNFa 24 hours


title: naïve_1


title: 9345344075_A

description: replicate 2

source_name: HT29 mock2 vehicle 24h -2


title: WT1_H2B

description: WT1 MEF


title: 39_2


title: RNAseq_KO3

description:
total RNA
RNA_counts.txt


title: 9345344071_K

description: replicate 2

source_name: HT29 ERb2 vehicle 2h -2


title: 9345344071_J

description: replicate 2

source_name: HT29 mock2 TNFa 2h -2


title: WT8_macroH2A2 input

description: WT3 MEF


title: 9345344071_H

description: replicate 1

source_name: HT29 ERb2 TNFa 24h -1


title: RNAseq_KO2

description:
total RNA
RNA_counts.txt


title: WT7_macroH2A2 input

description: WT2 MEF


title: WT6_macroH2A2 input

description: WT1 MEF


title: 37_2

value: Activated at 37 C


title: RNAseq_KO1

description:
total RNA
RNA_counts.txt


title: 9345344071_I

description: replicate 2

source_name: HT29 mock2 vehicle 2h -2


title: 37_3


title: WT2RS_macroH2A1 input

description: WT3 MEF


title: 37_1


title: RNAseq_WT4

description:
total RNA
RNA_counts.txt


title: MCA/1956(MC38)_TREM2_WT_2

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description:
meta_single_cell_2_macs.tsv
meta_single_cell_2_lymphoid.tsv

data_processing:
Cellranger cell count was used to align samples to the reference mm10 genome, quantify and filter reads with a quality score below 30.  The Seurat package (Butler et al., 2018) in R was used for subsequent analysis. Cells with mitochondrial content greater than 12.5% and with less than 1100 genes were removed. Cells identified as doublets or mutliplets based on gene expression signatures, when more than one cell population-specific marker gene was highly expressed in one cell, were filtered out. Filtered data were normalized using a scaling factor of 10,000, nUMI was regressed with a negative binomial model, and data was log transformed. The highly variable genes were selected using the FindVariableFeatures. Principal component analysis was performed using the top 3000 variable genes. Clustering was performed using the FindClusters function. UMAP was used to project cells into two dimensions using 20 first principal components. For myeloid cells re-clustering we chose clusters that were identified as myeloid cell and macrophages (either CX3CR1+ or Nos2+). For this cells we performed normalization, found variable genes and performed PCA, UMAP and clustering as descibed above. All vizualization was done with ggplot2 R package (Wickham, 2016), heatmaps were done with Phantasus website (https://artyomovlab.wustl.edu/phantasus/).
Genome_build: mm10
Supplementary_files_format_and_content: h5 matrices contain cellranger-created filtered UMI counts per cell per gene. Meta tables contain aggregated samples for two experiments, and have information about projection and clustering for total CD45 cells, myeloid cells and lymphoid cells (experiment 2 only) separately, as indicated in the corresponding sample description field.

extract_protocol:
Live CD45+ cells were sorted from processed tumors.
Using the Chromium Single Cell 3’ Reagent Kit v3 User Guide, single cell suspensions went through a GEM generation and barcoding, followed by GEM RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium™ Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The cDNA libraries were then sequenced on the Illumina NovaSeq S4.  A median sequencing depth of 50,000 reads/cell was targeted for each sample.

tag: tumor model

value: immune cells from tumor microenvironment


title: 9345344071_G

description: replicate 1

source_name: HT29 ERb2 vehicle 24h -1


title: WT1RS_macroH2A1 input

description: WT2 MEF


title: RNAseq_WT1

description:
total RNA
RNA_counts.txt


title: MCA/1956(MC38)_TREM2_WT_1


title: WT8_macroH2A2

description: WT3 MEF

value: macroH2A2 (abcam, ab102126)


title: RNAseq_WT2

description:
total RNA
RNA_counts.txt


title: WT1_macroH2A1 input

description: WT1 MEF


title: MCA/1956(MC38)_TREM2_KO_2


title: scRNAseq_KO4

description:
Whole cell
Cell ranger V2.0 based mapping and filtering

source_name: olfactory epithelium


title: scDamID_batch1_DamOnly_018

city: Berkeley

first: Nicolas

last: Altemose

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

description:
38
NA018
hg38_100kb_UniqueFragmentCounts.tsv

data_processing:
Library strategy: DamID
Bulk and single-cell DamID reads were demultiplexed using Illumina’s BaseSpace platform to obtain fastq files for each sample.
DamID and Illumina adapter sequences were trimmed off using trimmomatic (v0.39; Bolger et al. 2014; ILLUMINACLIP:adapters-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20, where adapters-PE.fa is:\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>Dam\nGGTCGCGGCCGAGGA\n>Dam_rc\nTCCTCGGCCGCGACC).
Trimmed reads were aligned to a custom reference (hg38 reference sequence plus the Dam-LMNB1 and m6A-Tracer plasmid sequences) using BWA-MEM (v0.7.15-r1140, Li 2013). Alignments with mapping quality 0 were discarded using samtools (v1.9, Li et al. 2009).
The hg38 reference sequence was split into simulated DpnI digestion fragments by reporting all intervals between GATC sites (excluding the GATC sites themselves), yielding 7180359 possible DpnI fragments across the 24 chromosome assemblies. The number of reads overlapping each fragment was counted using bedtools (v2.28; Quinlan et al. 2010). For single-cell data, the number of DpnI fragments with non-zero coverage was reported within each non-overlapping bin in the genome (28163 total 100 kb bins, after excluding unmappable regions with zero coverage in any cell).
For bulk data, the number of read pairs overlapping each 100 kb bin was reported. For bulk data, Dam-LMNB1 vs DamOnly enrichment was computed using Deseq2 in each 100 kb bin (Love et al. 2014). For single-cell data, the expected background coverage in each bin was computed as n(m/t), where n is the number of unique fragments sequenced from that cell, m is the number of bulk Dam-only read pairs mapping to that bin, and t is the total number of mapped bulk Dam-only read pairs. Single-cell normalization was computed either as a ratio of observed to expected coverage (for browser visualization and comparison to bulk data), or as their difference (for classification and coverage distribution plotting).
For bulk RNA-seq data, adapters were trimmed using trimmomatic (v0.39; Bolger et al. 2014; ILLUMINACLIP:adapters-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, where adapters-PE.fa is:\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). Transcript quantification was performed using Salmon (Patro et al. 2017) with the GRCh38 transcript reference. Differential expression analysis was performed using the voom function in limma (Ritchie et al. 2015). Differential expression was called based on logFC significantly greater than 1 and adjusted p-value < 0.01.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: hg38_100kb_UniqueFragmentCounts.tsv
Supplementary_files_format_and_content: DamMutantComparison_Counts.tsv
Supplementary_files_format_and_content: RNAseq_Counts_GeneBySample.csv

source_name: HEK293T cells

growth_protocol: HEK293T cells (CRL-3216, ATCC, Manassas, VA; validated by microsatellite typing & mycoplasma tested, at passage number <10) were cultured in DMEM plus 10%FBS and 1X Penicillin-Streptomycin at 37C with 5% CO2.

extract_protocol:
Cells were processed within nanoliter reaction chambers on a custom PDMS microfluidic device, following the reagents and incubation times of the in-tube single-cell DamID protocol (Kind et al. 2015) with minor modifications (addition of 0.2% Tween-20 to prevent enzyme adhesion). Amplified DNA from each individual cell was flushed out of the device and transferred to 0.2 ml tubes, where library preparation took place.
Single-cell sequencing libraries were prepared from the DamID amplified DNA using an NEBnext UltraII DNA Library Prep Kit for Illumina (samples 001-018) or an NEBnext UltraII FS Kit (samples A01-D10).

treatment_protocol: Human HEK293T cells were transiently transfected with Dam-LMNB1 plus m6A-Tracer using FuGene HD, induced using 1 mM Shield-1 ligand for 20 hours prior to harvesting as a single-cell suspension.

tag: transfection

value: DamV133A + m6A-Tracer


title: WT7_macroH2A2

description: WT2 MEF


title: scRNAseq_KO3


title: MCA/1956(MC38)_TREM2_KO_1


title: RNAseq_WT3

description:
total RNA
RNA_counts.txt


title: scDamID_batch1_DamOnly_017

description:
37
NA017
hg38_100kb_UniqueFragmentCounts.tsv

tag: cell line


title: B cells JQ1 2hr 1

city: New York

source_name: Purified Primary B cells

value: B cells stimulated with LPS


title: MCA/1956(MC38)_CTRL_2


title: 9462064009_B

description: replicate 1

source_name: SW480 mock2 TNFa 2h -1

value: 10ng/mL TNFa 2 hours


title: 9345344071_B

description: replicate 1

source_name: HT29 mock2 TNFa 2h -1


title: 9345344071_D

description: replicate 1

source_name: HT29 ERb2 TNFa 2h -1


title: scDamID_batch1_DamOnly_016

description:
36
NA016
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNAseq_KO2

tag: tissue

value: olfactory epithelium


title: 9345344071_A

description: replicate 1

source_name: HT29 mock2 vehicle 2h -1

value: vehicle 2 hours


title: WT6_macroH2A2

description: WT1 MEF

source_name: murine embryonic fibroblast

value: murine embryonic fibroblast

tag: chip antibody


title: WT2RS_macroH2A1

description: WT3 MEF

value: SV40 transformed

value: macroH2A1 (abcam, ab183041)


title: 9345344071_E

description: replicate 1

source_name: HT29 mock2 vehicle 24h -1


title: 9345344071_C

description: replicate 1

source_name: HT29 ERb2 vehicle 2h -1


title: 9345344071_F

description: replicate 1

source_name: HT29 mock2 TNFa 24h -1


title: scRNAseq_KO1


title: scDamID_batch1_015

description:
35
NA015
hg38_100kb_UniqueFragmentCounts.tsv

value: DamV133A-LMNB1 + m6A-Tracer


title: WT1RS_macroH2A1

description: WT2 MEF

value: Lsh+/+


title: MCA/1956(MC38)_CTRL_1


title: MCA/1956(MC38)_aTREM2-aPD1_2

value: aPD1 + aTREM2 antibodied


title: scDamID_batch1_014

description:
34
NA014
hg38_100kb_UniqueFragmentCounts.tsv


title: WT1_macroH2A1

description: WT1 MEF


title: scRNAseq_WT4

value: wild type


title: scRNAseq_WT3


title: MCA/1956(MC38)_aTREM2-aPD1_1


title: KO3_H2B input

description: KO3 MEF

value: Lsh-/-


title: scDamID_batch1_013

description:
33
NA013
hg38_100kb_UniqueFragmentCounts.tsv


title: scDamID_batch1_012

description:
32
NA012
hg38_100kb_UniqueFragmentCounts.tsv


title: MCA/1956(MC38)_aTREM2_2

value: aTREM2 antibody


title: scRNAseq_WT2


title: KO2_H2B input

description: KO2 MEF


title: scRNAseq_WT1


title: MCA/1956(MC38)_aTREM2_1


title: scDamID_batch1_011

description:
31
NA011
hg38_100kb_UniqueFragmentCounts.tsv


title: KO1_H2B input

description: KO1 MEF


title: KO3_H2B

description: KO3 MEF

value: H2B (abcam, ab1790)


title: scDamID_batch1_010

description:
30
NA010
hg38_100kb_UniqueFragmentCounts.tsv


title: MCA/1956(MC38)_aPD1_2

value: aPD1 antibody

value: immune cells from tumor microenvironment


title: MCA/1956(MC38)_aPD1_1


title: scDamID_batch1_009

description:
29
NA009
hg38_100kb_UniqueFragmentCounts.tsv


title: scDamID_batch1_008

description:
28
NA008
hg38_100kb_UniqueFragmentCounts.tsv


title: BMDMs IFNy 3

description: Heme-albumin preparation protocol: Hemin (heme-chloride) was obtained from Sigma (51280), and ZnPP was obtained from Frontiers (FSIZn625-9). The porphyrins were dissolved in 10 ml of NaOH (100 mM) at 37°C, followed by addition of 10 ml of 20% human serum albumin (CSL Behring AG). After 1 hour of incubation at 37°C, the pH of the solution was adjusted to pH 7.4 using ortho-phosphoric acid, and the final volume was brought to 25 ml with saline solution. The porphyrin-albumin solutions were sterile-filtered (0.22 µm) and used immediately.

data_processing:
Reads were aligned to the reference genome  using STAR (v2.7.0e).
The quality of alignment was evaluated using Samtools (v1.9).
Counts were obtained using the featureCounts function of the Rsubread package (v1.22.2).
Genome_build: Ensembl GRCm38.p5 Release 91
Supplementary_files_format_and_content: Output from feautrecount: table with raw count data of every genes (row) for each sample (column)

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells were obtained from the femurs and tibias of 8- to 10-week-old mice. The bone marrow murine stem cells were expanded and differentiated in RPMI medium supplemented with 10% FCS in the presence of recombinant mouse M-CSF (PeproTech 315-02-100UG, lot 0914245) at 10 ng/ml for 7 days

extract_protocol:
RNeasy Micro kit (Qiagen, Hombrechtikon, Switzerland) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA samples using the Illumina TruSeq RNA stranded kit following the manufacturer’s instructions.

treatment_protocol: Macrophages were polarized to the M1 phenotype with 10 ng/ml interferon gamma (IFNγ, PeproTech, 214-14-2UG, lot 111249), to the M2 phenotype with 10 ng/ml interleukin 4 (IL-4, PeproTech, 315-05-20UG, lot 061398) or to erythrophagocytes like with 200 µM or 400 µM  heme-albumin

value: Bone marrow derived macrophages

value: 10 ng/ml interferon gamma (IFNγ)


title: KO2_H2B

description: KO2 MEF


title: scDamID_batch1_007

description:
27
NA007
hg38_100kb_UniqueFragmentCounts.tsv


title: BMDMs IFNy 2


title: KO1_H2B

description: KO1 MEF


title: 39_1

source_name: Mouse splenic CD4+ T cells

value: Activated at 39 C


title: BMDMs IFNy 1


title: scDamID_batch1_006

description:
26
NA006
hg38_100kb_UniqueFragmentCounts.tsv


title: BMDMs IL-4 3

value: 10 ng/ml interleukin 4 (IL-4)


title: KO7_macroH2A2 input

description: KO2 MEF


title: scDamID_batch1_005

description:
25
NA005
hg38_100kb_UniqueFragmentCounts.tsv


title: Meniscus_24W_OA3

city: Haikou

first: Hui

last: Huang

address: 19 Xiuhua Road, Xiuying District

institute: Hainan Provincial People's Hospital

description: After 24 weeks after the pig underwent anterior cruciate ligament surgery, the meniscus tissue was taken to extract RNA, and then gene chip detection was performed

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 7 out of 14 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

organism: Sus scrofa

source_name: Meniscus, 24W, OA3

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cryopulverization of tissue using the Biopulverizer

extract_protocol: Take an appropriate amount (50-100mg) of properly preserved tissue samples, use BioPulverizerTM to freeze and crush the tissue, add 1ml of RNA extraction reagent TRIzol (Invitrogen), use Mini-Bead-Beater-16 to homogenize and extract RNA. Use NanoDrop-1000 spectrophotometer to quantify RNA, and perform denaturing agarose gel electrophoresis with formaldehyde electrophoresis reagent to detect RNA purity and integrity.

value: meniscus

tag: gender

value: male

tag: age

value: 6 to 7 months

tag: group

value: experimental


title: Meniscus_24W_OA7

source_name: Meniscus, 24W, OA7


title: Meniscus_24W_OA6

source_name: Meniscus, 24W, OA6


title: BMDMs IL-4 2

tag: cell type


title: scDamID_batch1_004

description:
24
NA004
hg38_100kb_UniqueFragmentCounts.tsv

value: DamV133A-LMNB1 + m6A-Tracer


title: Meniscus_24W_OA4

source_name: Meniscus, 24W, OA4


title: Meniscus_24W_OA2

source_name: Meniscus, 24W, OA2


title: scDamID_batch1_003

description:
23
NA003
hg38_100kb_UniqueFragmentCounts.tsv

source_name: HEK293T cells


title: Meniscus_24W_OA1

source_name: Meniscus, 24W, OA1


title: KO8_macroH2A2 input

description: KO3 MEF

value: murine embryonic fibroblast

value: SV40 transformed


title: BMDMs Heme-alb 400 2

value: 401 µM  heme-albumin


title: KO1_macroH2A1 input

description: KO1 MEF

value: Lsh-/-


title: BMDMs Heme-alb 400 3

value: 402 µM  heme-albumin


title: KO8_macroH2A2

description: KO3 MEF

value: macroH2A2 (abcam, ab102126)


title: Meniscus_24W_OA5

source_name: Meniscus, 24W, OA5


title: scDamID_batch1_002

description:
22
NA002
hg38_100kb_UniqueFragmentCounts.tsv


title: scDamID_batch1_001

description:
21
NA001
hg38_100kb_UniqueFragmentCounts.tsv


title: BMDMs Heme-alb 400 1

value: 400 µM  heme-albumin


title: Meniscus_24W_Sham7

description: After 24 weeks of sham operation in pigs, meniscus tissues were taken to extract RNA, and then gene chip detection was performed

source_name: Meniscus, 24W, Sham7

value: control


title: 72hrSym_3

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Sequenced reads were mapped to Coral reference transcriptome: using bowtie2 with DEFAULT parameters
transcript abundances were estimated from libraries mapped to the refrenece transcriptome using RSEM
Raw counts were analysed to infer differential expression in edgeR package in the R environment. Symbiotic samples at 3, 12, 48 and 72 h were compared to their corresponding control samples.
Gene co-expression network was constructed by application of RIF and PCIT algorithms
Genome_build: Coral reference transcriptome: http://aten.reefgenomics.org/download/
Genome_build: Symbiont reference transcriptome C. goreaui (Levin et al., 2016):  https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE72763&format=file&file=GSE72763%5FMI%5Ftranscriptome%2Efasta%2Egz
Supplementary_files_format_and_content: tab-delimited text files include expression values in CPM for each Sample

organism:
Acropora tenuis
Cladocopium goreaui

source_name: infected coral larvae_72hpi

growth_protocol: Coral larvae were raised in FSW

extract_protocol:
Both infected and non-infected "control" larvae were removed from FSW, flash frozen in liquid Nitrogen and lysed twice for 20s at 4.0 m s−1 in Lysing Matrix D tubes (MP Biomedicals, Australia) containing 960 µL of lysis/binding solution plus 80 µL of the Plant RNA Isolation Aid (Ambion, USA) on a FastPrep®-24 Instrument (MP Biomedicals, Australia). RNA was bound to the columns, washed multiple times, eluted in 40 μL of RNase-free water and stored at -80°C . Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exposure of symbiont-free larvae to native algal symbionts (normally found in the adult) and sampling larvae at 3, 12, 48 and 72 hours post colonisation

value: Cladocopium goreaui; ITS2 type C1

value: infected coral larvae

value: 72hr post infection


title: Meniscus_24W_Sham6

source_name: Meniscus, 24W, Sham6


title: KO6_macroH2A2 input

description: KO1 MEF

source_name: murine embryonic fibroblast


title: 72hrSym_2


title: KO2RS_macroH2A1 input

description: KO3 MEF


title: KO7_macroH2A2

description: KO2 MEF


title: KO6_macroH2A2

description: KO1 MEF


title: BMDMs Heme-alb 200 2

value: Bone marrow derived macrophages

value: 200 µM  heme-albumin


title: Meniscus_24W_Sham5

source_name: Meniscus, 24W, Sham5

value: meniscus

value: male


title: KO1RS_macroH2A1 input

description: KO2 MEF


title: Meniscus_24W_Sham4

source_name: Meniscus, 24W, Sham4

value: 6 to 7 months


title: 72hrSym_1


title: Meniscus_24W_Sham3

source_name: Meniscus, 24W, Sham3


title: KO2RS_macroH2A1

description: KO3 MEF

value: macroH2A1 (abcam, ab183041)


title: BMDMs IL-4 1

source_name: Bone marrow derived macrophages

value: 10 ng/ml interleukin 4 (IL-4)


title: BMDMs Heme-alb 200 1


title: BMDMs Heme-alb 200 3


title: KO1RS_macroH2A1

description: KO2 MEF

value: murine embryonic fibroblast

value: SV40 transformed


title: 48hrSym_3

source_name: infected coral larvae_48hpi

value: 48hr post infection


title: BMDMs Control 3


title: 48hrSym_2


title: KO1_macroH2A1

description: KO1 MEF

value: Lsh-/-


title: 48hrSym_1


title: Mock 5hpf Rep-3

city: Warsaw

middle: Lanny

last: Winata

state: Mazovia

address: 4 Ks. Trojdena

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description:
PolyA RNA
Replicate 3

data_processing:
Base-calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
The first 12 nucleotides of read 1, containing the UMI sequence, were extracted and added to the sequence identifier using UMI-tools v. 1.0.0.
Low-quality sequences and adapter content were trimmed with cutadapt v. 2.4.
Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverLmax 0.6.
Alignments were de-duplicated based on their Unique Molecular Identifier sequence using UMI-tools v. 1.0.0.
De-duplicated alignments were counted per exon on the gene-level with the htseq-count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation.
Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: HTSeq counts.tsv files were generated with htseq-count script, they contain counts for each gene for each sample in tab-delimited format; normalized_counts files were generated with DESeq2, they contain library-size normalized read counts for each gene for every sample from each time point in tab-delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp_crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
25 embryos each (for both StCsm and mock injected) were pooled at 128 cell stage, 5 hpf and 24 hpf from 3 biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution (Invitrogen) according to the manufacturer’s protocol. RNA was further purified using Zymo RNA Clean and Concentrator-5 kit according to manufacturer's protocol.
1.5 ug of total RNA was subjected to Lexogen poly(A) RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA-Seq Library Prep Kit according to the Lexogen manufacturer’s protocol.

treatment_protocol: Zebrafish embryos from three different mating pairs of Tg(ddx4:ddx4-EGFP) females with casper males were pooled during collection. D16A-StCsm(EGFP) was diluted with water for injection (1:1 v/v) up to a concentration of 0.7mg/ml. For mock injection, Tris storage buffer (10mM Tris-HCl pH8.5, 300mM Nacl, 1mM DTT, 0.1mM EDTA, 50% glycerol) was also diluted in the similar manner. 1nl of either StCsm (EGFP) solution (0.7ng) or buffer alone were injected into the yolk of embryos at the 1-cell stage. In total, three independent injections were performed. 25 embryos (for both StCsm and mock injected) per replica set per time point were frozen in liquid nitrogen, stored at -80℃, and processed together.

value: ABTL Tg(ddx4:ddx4-EGFP)

value: whole embryo

tag: condition

value: Mock

value: 5 hpf


title: BMDMs Control 2


title: REN-siRNA YB-1 rep#1

city: Concord, NSW

first: Kaitao

last: Lai

state: New South Wales

address: ANZAC Research Institute, Hospital Rd, Concord

department: Faculty of Medicine and Health

institute: Anzac Research Institute, The University Of Sydney

data_processing:
Read were aligned to hg38 using STAR version 2.5.3a
SNPs were called using freebayes version 1.3.1
SNPs were annotated using bcftools version 1.9
RNA-Seq data analysis performed using DESeq2 package
Genome_build: hg38

source_name: Mesothelioma Cell Line

growth_protocol: Cells were maintained in Roswell Park Memorial Institute 1640-GlutaMAX™ (RPMI) medium supplemented with 10% heat inactivated foetal bovine serum (ThermoFisher Scientific) in a humidified atmosphere (5% CO2 and 37 °C). Cells were routinely monitored for mycoplasma and their identity confirmed by short tandem repeat profiling (Australian Genome Research Facility).

extract_protocol:
TRIzol extraction was conducted 96 h after transfection. DNA was removed using a TURBO DNA-free kit (Invitrogen). All RIN>8 (bioanalyser), 260/280 >1.8 (nanophotometre)
TruSeq stranded RNA sample preparation protocol (Illumina). cDNA synthesis: mRNA was purified via oligo(dT) beads, fragmented with divalent cations and heat, 1st strand of cDNA was randomly primed, 2nd strand of cDNA was synthesised. cDNA library preparation: DNA fragment end repair (blunt ending of DNA fragments), 3' Adenylation of DNA fragments, Sequencing adapter ligation (T-A pairing of adapter and DNA fragments), Amplificatio of library via PCR

treatment_protocol: Cells (1x10^5) were reverse transfected with 5 nM control or YB-1 siRNA (three replicates)

value: REN

tag: subtype

value: Epithelioid subtype


title: REN-siRNA YB-1 rep#2


title: REN-siRNA YB-1 rep#3


title: BMDMs Control 1

value: Bone marrow derived macrophages


title: Macrophages SPTA aCD40 3

source_name: Non-parenchymal liver cells enriched for F4/80 positive macrophages

extract_protocol:
The abdominal cavity of a living, deeply anesthetized mouse was opened, and the portal vein was catheterized for in situ liver perfusion and digestion with 50 ml of 0.06 U/ml collagenase B buffered solution (Roche, 11088815001). Once digested, livers were dissected out and the mouse was sacrificed. The digested livers were then mechanically disaggregated in a petri dish on ice and filtered through a 100 μm pore cell strainer. The cell suspensions were centrifuged twice at 60 x g for 2 min at 4°C, and the pellets were discarded. The supernatants were then centrifuged at 300 x g for 5 min at 4°C to obtain a pellet of nonparenchymal liver cells containing liver macrophages. To select for F4/80+ macrophages from liver cell suspensions, Dynabeads Sheep anti-Rat IgG (Invitrogen, 11035), in combination with purified rat anti-mouse F4/80 antibody (BD Pharmingen, 0.5 mg/ml, 565409) ), and a DynaMag™-2 Magnet (Thermo Fisher Scientific, 12321D) were used according to the manufacturer's protocol (Invitrogen)
RNeasy Micro kit (Qiagen, Hombrechtikon, Switzerland) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA samples using the Illumina TruSeq RNA stranded kit following the manufacturer’s instructions.

treatment_protocol: Saline i.p. or agonistic anti-CD40 antibody i.p. 20 mg/kg 30h injection

value: Liver

tag: genotype

value: Spta sph/sph

value: Anti-CD40 i.p. 20 mg/kg 30h


title: 12hrSym_3

source_name: infected coral larvae_12hpi

value: Cladocopium goreaui; ITS2 type C1

value: infected coral larvae

value: 12hr post infection


title: 12hrSym_2


title: Mock 5hpf Rep-2

description:
PolyA RNA
Replicate 2

tag: developmental stage


title: 12hrSym_1


title: Macrophages SPTA aCD40 1

value: Non-parenchymal liver cells enriched for F4/80 positive macrophages

tag: treatment


title: REN-siRNA Control rep#3


title: Macrophages SPTA aCD40 2


title: REN-siRNA Control rep#1


title: Meniscus_24W_Sham1

source_name: Meniscus, 24W, Sham1

value: meniscus

value: male

value: 6 to 7 months

value: control


title: Mock 24hpf Rep-3

description:
PolyA RNA
Replicate 3

value: ABTL Tg(ddx4:ddx4-EGFP)

value: whole embryo

value: 24 hpf


title: REN-siRNA Control rep#2

value: REN


title: Meniscus_24W_Sham2

source_name: Meniscus, 24W, Sham2


title: Mock 24hpf Rep-2

description:
PolyA RNA
Replicate 2

value: Mock


title: 3hrSym_2

source_name: infected coral larvae_3hpi

value: 3hr post infection


title: Mock 24hpf Rep-1

description:
PolyA RNA
Replicate 1


title: Macrophages WT aCD40 3

value: Liver

value: Spta wt/wt


title: Macrophages WT aCD40 2

value: Anti-CD40 i.p. 20 mg/kg 30h


title: 3hrSym_1

value: Cladocopium goreaui; ITS2 type C1


title: VMC23-siRNA YB-1 rep#3

value: Epithelioid subtype


title: VMC23-siRNA YB-1 rep#2


title: Mock 5hpf Rep-1

description:
PolyA RNA
Replicate 1

value: 5 hpf


title: Macrophages WT aCD40 1

value: Non-parenchymal liver cells enriched for F4/80 positive macrophages


title: Mock 128 Rep-3

description:
PolyA RNA
Replicate 3

value: 128 cells


title: VMC23-siRNA YB-1 rep#1


title: 11559_wb-3

city: Ithaca

first: Olga

last: Lastovetsky

state: NY

address: 334 Plant Science Building, 236 Tower Rd, Cornell University

institute: Cornell University

description:
processed data file: pre-contact_fungal_atcc11559.count
processed data file: pre-contact_fungal_atcc11559_results

data_processing:
Reads were quality controlled using FASTQ and trimmed with Trimmomatic to eliminate low quality reads and Illumina adapters
reads were aligned to the fungal genomes of R. microsporus ATCC 52813 (GenBank accession JOSV00000000) and R. microsporus ATCC 11559 (GenBank MCOJ00000000) using TopHat with following parameters tophat -p 11 -o outputdirectory -G genome.gff3 --transcriptome-index xxx --no-novel-juncs genomefile xxx_R1_paired.fq xxx_R2_paired.fq. Bacterial reads were aligned to genome of Burkholderia sp. B13 (FTPM01000001-FTPM01000002) using bwa with the following parameters: bwa mem -t 8 GENOME.fa -t 8 xxx.fq > xxx.sam
Fungal transcript abundances were quantified with CuffDiff, bacterial transcript abundances measured with RSEM, and the counts files used for differential expression analysis with EdgeR
Genome_build: R. microsporus ATCC 52813 NCBI accession number: JOSV00000000
Genome_build: R. microsporus ATCC 11559 NCBI accession number: MCOJ00000000
Genome_build: Burkholderia sp. B13 European Nucleotide Archive (ENA) accession FTPM01000001-FTPM01000002
Supplementary_files_format_and_content: tab-delimeted text file with read counts generated by CuffDiff  or RSEM which was then used for differential expression analysis with EdgeR. EdgeR-generated tab-delimited text file with fold change, p- and and false discovery rate-values for all the genes .

organism:
Rhizopus microsporus ATCC 52813
Burkholderia sp. b13

source_name: vegetative mycelium, bacteral cells

extract_protocol:
Total RNA was extracted with the Ambion ToTALLY Total RNA Isolation Kit (Life Technologies, Grand Island, NY) and rRNA was removed with RiboZero Magnetic Gold Kit (Epicentre, Madison, WI)
RNA sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina®

value: vegetative mycelium, bacteral cells

tag: growth stage

value: 56h post inoculation


title: 11559_wb-2


title: Mock 128 Rep-2

description:
PolyA RNA
Replicate 2


title: VMC23-siRNA Control rep#3


title: Macrophages SPTA CTRL 3

value: Spta sph/sph

value: Saline i.p.


title: 3hrSym_3

value: infected coral larvae


title: Macrophages SPTA CTRL 2


title: VMC23-siRNA Control rep#2


title: Csm 5hpf Rep-3

description:
PolyA RNA
Replicate 3

value: ABTL Tg(ddx4:ddx4-EGFP)

value: whole embryo

value: Csm complex targeted against the EGFP transcript


title: Macrophages SPTA CTRL 1


title: Macrophages WT CTRL 3


title: 11559_wb-1


title: Csm 5hpf Rep-2

description:
PolyA RNA
Replicate 2


title: 13f_wb-2

description:
processed data file: pre-contact_fungal_atcc52813.count
processed data file: pre-contact_fungal_atcc52813_results

value: 50h post inoculation


title: Csm 5hpf Rep-1

description:
PolyA RNA
Replicate 1


title: MSTO-siRNA YB-1 rep#3

value: Biphasic subtype

tag: genotype/variation

value: Homozygous deletion of CDKN2A (PubMed=16630136) and LATS2 (PubMed=21245096)


title: Macrophages WT CTRL 2

value: Liver

value: Spta wt/wt


title: 13f_wb-1

tag: strain


title: MSTO-siRNA YB-1 rep#2


title: Csm 24hpf Rep-3

description:
PolyA RNA
Replicate 3

value: 24 hpf


title: Macrophages WT CTRL 1


title: MSTO-siRNA YB-1 rep#1


title: Csm 24hpf Rep-2

description:
PolyA RNA
Replicate 2


title: bulkRNAseq_untreated_rep2

description:
20
HEK_untreated_RNA_2
RNAseq_Counts_GeneBySample.csv

source_name: HEK293T cells


title: bulkRNAseq_untreated_rep1

description:
19
HEK_untreated_RNA_1
RNAseq_Counts_GeneBySample.csv


title: Macrophages SPTA

data_processing:
The Cell Ranger Single-Cell Software Suite was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data. Cell Ranger Count (version 3.0.1) generated a digital expression matrix for each sample and filtered the cell-containing droplets from empty droplets.
The two filtered digital expression matrices were then merged into one using CellRanger Aggr and then further analyzed using R (v3.6.1) [https://www.R-project.org/].
Supplementary_files_format_and_content: First processed data file are the raw and filtered count matrix obtained after Cell Ranger Count and CellRangerr Agg containing count for every gene in each barcoded cell.
Cell quality control was performed using the scater R package (v1.12.2). Cells with a high mitochondrial gene ratio count were excluded from the data set (1506 out of 18,633 cells were removed). They were determined by the isOutlier function of the scater package, which placed the cut-off at 53% (at 3 median absolute deviation (MAD) above median of all cells).
Normalization was performed using the deconvolute normalization algorithm implemented in the scran R package (v1.12.1), using the computeSumFactors function on cells clustered with quickCluster function from the same package. After normalization, principal component analysis (PCA) was performed using the denoisePCA function of the same package to reduce the number of dimensions representing each cell. Based on the first 10 PCA, a shared nearest neighbor graph was built with the buildSNNGraph function, and the Louvain algorithm was performed to identify cell clusters using the cluster_louvain function implemented in the igraph package (v1.2.4.1).
Supplementary_files_format_and_content: Second processed data file is an .rds file containing single cell experiment object (sce) of the data after quality contorl, normalization, dimensionality reduction and clustering
Genome_build: Ensembl GRCm38.p5 Release 91
Supplementary_files_format_and_content: barcodes.tsv.gz: List of all unique 10 x barcode with sample origin (-1 or -2)
Supplementary_files_format_and_content: features.tsv.gz: Identifier and name of all features
Supplementary_files_format_and_content: matrix.mtx.gz: count expression matrix
Supplementary_files_format_and_content: sce-SPTAmerged-Final.rds: .rds file containing single cell experiment object (sce) of the data after quality contorl, normalization, dimensionality reduction and clustering

extract_protocol:
The abdominal cavity of a living, deeply anesthetized mouse was opened, and the portal vein was catheterized for in situ liver perfusion and digestion with 50 ml of 0.06 U/ml collagenase B buffered solution (Roche, 11088815001). Once digested, livers were dissected out and the mouse was sacrificed. The digested livers were then mechanically disaggregated in a petri dish on ice and filtered through a 100 μm pore cell strainer. The cell suspensions were centrifuged twice at 60 x g for 2 min at 4°C, and the pellets were discarded. The supernatants were then centrifuged at 300 x g for 5 min at 4°C to obtain a pellet of nonparenchymal liver cells containing liver macrophages. To select for F4/80+ macrophages from liver cell suspensions, Dynabeads Sheep anti-Rat IgG (Invitrogen, 11035), in combination with purified rat anti-mouse F4/80 antibody (BD Pharmingen, 0.5 mg/ml, 565409) ), and a DynaMag™-2 Magnet (Thermo Fisher Scientific, 12321D) were used according to the manufacturer's protocol (Invitrogen). The purity of the separated cells was tested by detecting F4/80 positive cells by FACS.
Nonparenchymal liver cell suspension enriched for F4/80+ macrophages were processed for library preparation according to the 10x Genomics Chromium Single Cell 3’ v3 Reagent Kit instruction guide. Briefly, sample volume was adjusted to a target capture of 10,000 cells and loaded onto the 10x Genomics single-cell-A chip. After droplet generation, samples were subjected to reverse transcriptase and the barcoded cDNA was further amplified for 11 cycles (adjusted for a cell recovery of >6000,  as suggested by the 10x Genomic user guide). cDNA quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). cDNA strands were then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA, and sample index was added during sample index PCR (set for 13 cycles, as recommended by 10X Genomics user guide to correlate with a cDNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). Libraries were pooled in equimolar amounts and sequenced using the Illumina NovaSeq 6000 system according to 10X Genomics recommendations: paired-end reads, R1=28 cycles, i7=8 cycles and R2=91 cycles. Sequencing depth was targeted for 50,000 reads per cell in both samples.


title: MSTO-siRNA Control rep#3


title: Mock 128 Rep-1

description:
PolyA RNA
Replicate 1

value: Mock


title: Csm 24hpf Rep-1

description:
PolyA RNA
Replicate 1


title: VMC23-siRNA Control rep#1

value: Epithelioid subtype


title: Macrophages WT

value: Non-parenchymal liver cells enriched for F4/80 positive macrophages


title: 13f_wb-3

value: vegetative mycelium, bacteral cells


title: MSTO-siRNA Control rep#1


title: bulkRNAseq_m6ATracer_rep1

description:
17
HEK_mTracer_RNA_1
RNAseq_Counts_GeneBySample.csv


title: MSTO-siRNA Control rep#2


title: Csm 128 Rep-3

description:
PolyA RNA
Replicate 3

value: 128 cells


title: Csm 128 Rep-2

description:
PolyA RNA
Replicate 2


city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 36 weeks of age, biological rep4

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: PiZ mouse model deleted for Chop, 36-week old mouse liver

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
Libraries were sequenced on a NovaSeq 6000 sequencing system using an S1, 100 cycles flow cell (Illumina Inc.).
Amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode with a read length of 100 bp.

treatment_protocol: Animal procedures were performed in accordance to regulations of the Italian Ministry of Health. All the mice were maintained on a C57/BL6 background.

value: MALE

value: PiZ mouse model deleted for Chop

value: 36-week old

value: liver