title: TR1_d2_CRE2

status: Public on Mar 15 2018

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description: SEB-stimulated Txnrd1-deficient

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped and annotated to GRCm38.PatchesSkipped Version 2015-06-2 STAR with cmdOptions --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method
Genome_build: GRCm38.PatchesSkipped Version 2015-06-25
Supplementary_files_format_and_content: the processed data file includes Gene Identifier, gene name, transcript id, type, description, log2 Ratio, gfold (log2 Change), pValue, fdr, normalized count (TMM)

source_name: Spleen

growth_protocol: Vb8.1/8.2+CD8+ T cells were isolated from mouse spleen using MACS and FACS sorting

extract_protocol:
Cells were collected into Trizol (life technologies), phase separation was achieved by addition of chloroform (Sigma-Aldrich) and RNA was precipitated from the aqueous layer with isopropanol (Sigma-Aldrich) using glycogen (Roche) as a carrier.
The TruSeq RNA Stranded Sample Prep kit (Illumina) was used to construct the sequencing libraries. In brief, total RNA samples (100 ng) were poly-A enriched and reverse transcribed into double-stranded cDNA. TruSeq adapters were then ligated to double-stranded cDNA. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR and subsequently sequenced on the Illumina NextSeq 500 in single-end mode, 150 cycles at the Functional Genomics Center Zurich (FGCZ).

treatment_protocol: Mice were intraperitoneal injected with 100ug Staphilococcal enterotoxin B. After 2 days,  300k  Vb8.1/8.2+CD8+ T cells were sorted for RNA-seq

value: CD8+ T cells

value: Txnrd1-deficient (Txnrd1fl/fl;CD4-Cre)

value: SEB-stimulated


title: TR1_d2_WT2

type: SRA

description: SEB-stimulated WT

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: genotype

value: WT (Txnrd1fl/fl)

tag: treatment


title: TR1_d2_CRE1

description: SEB-stimulated Txnrd1-deficient


title: Drosophila nuclei sci-ATAC-seq

status: Public on Mar 16 2018

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

country: USA

institute: University of Arizona

description: Accessible genomic DNA

library_source: genomic

data_processing:
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to dm3 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromsomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Mapped reads to 2kb windows in the genome using custom python script.
After clustering cells, called peaks on clusters of cells using MACS2 v2.1.1.20160309.
Overlapped reads with summits of accessibility using custom python script.
Genome_build: dm3
Supplementary_files_format_and_content: ".2kbmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each 2kb window, remaining columns include counts of reads overlapping that site assigned to each barcode.
Supplementary_files_format_and_content: ".summitmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each hypersensitivity summit, remaining columns include counts of reads overlapping that site for each cell barcode.
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column2 = developmental stage of embryos and PCR plate that barcode represents.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Nuclei isolated from whole embryos

extract_protocol:
Whole embryos were fixed and nuclei were isolated (please see publication for more details).
Please see publication for details on library construction.

tag: tissue

value: whole embryos

tag: developmental stage

value: 2 to 4 hours after egg laying

value: 6 to 8 hours after egg laying

value: 10 to 12 hours after egg laying


title: TR1_d0_CRE1

description: Naive Txnrd1-deficient

value: Naive


title: TR1_d0_WT1

description: Naive WT


title: TR1_d0_CRE2

description: Naive Txnrd1-deficient


title: TR1_d2_WT1

description: SEB-stimulated WT


title: TR1_d0_WT2

description: Naive WT


title: WT_ABX_Jejunum_MM317-9

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 transcriptome (ENSEMBL v 81) using TopHat2.
Gene-level expression estimates were calculated using HTSeq.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: Jejunum

growth_protocol: Mice were housed at the University of Chicago animal facilities under specific pathogen-free (SPF) conditions, where cages were changed on a weekly basis; ventilated cages, bedding, food and water (non-acidified) were autoclaved before use, ambient temperature maintained at 23C, and 5% Clidox-S was used as a disinfectant. Experimental breeding cages were randomly housed on two different racks in the vivarium, and all cages were kept on automatic 12-h light/dark cycles. Animal husbandry for both SPF and germ free (GF) facilities, and experimental procedures were performed in accordance with Public Health Service policy and approved by the University of Chicago Institutional Animal Care and Use Committees.

extract_protocol:
Small and large intestine were removed and transferred into cold PBS. A piece (~ 5mm) of whole intestinal tissue (duodenum, jejunum, ileum and colon) was soaked in RNAlaterTM (Qiagen) at 4 ºC for 48 hours and then stored at -80 ºC until further analysis. For RNA extraction a Tissue-Tearor Homogenizer (Biospec) was used. RNA was prepared using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared using the TruSeq® Stranded Total RNA with Ribo-ZeroTM Gold kit (Illumina) and sequenced using 50- and 100-base pair single-end reading on a HiSeq 2500 and 4000 instruments, respectively (Illumina).

treatment_protocol:
TET2-/- mice were previously described (Moran-Crusio et al., 2011).
Mice were treated with an antibiotic cocktail as previously described 32. All antibiotics used are listed as follows (used concentration, company, catalog number). In detail, in the first week, mice received a daily intragastric gavage with 100 μL of a mixture of kanamycin (4 mg ml-1, Sigma-Aldrich, 60615), gentamicin (0.35 mg ml-1, Sigma-Aldrich, G1914), colistin (8500 U ml-1, Sigma-Aldrich, C4461), metronidazole (2.15 mg ml-1, Sigma-Aldrich, M3761), and vancomycin (0.45 mg ml-1, Sigma-Aldrich, V2002). For the following three weeks antibiotics were administered in the autoclaved (non-acidified) drinking water at 50-fold dilution except for vancomycin, which was maintained at 0.5 mg ml-1. Autoclaved (non-acidified) water was used to dissolve antibiotics. Antibiotic water was prepared fresh and replaced weekly.

tag: mouse id

value: WT

value: ABX


title: WT_ABX_Jejunum_MM317-8


title: BMDM LPS-EZH2_ChIPSeq

city: Shanghai

first: Xingli

last: Zhang

address: yueyang road 320

country: China

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences

description: stimulated for 2 h with LPS

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
005WIHS_EZH2_ucsctracks.bed represents the custom track for UCSC browser to see location of Intervals and Active Regions. It contains the locations and names of all Intervals (shown as orange bars) and Active Regions (green). It also contains the location and values of the Interval summits (purple).
Genome_build: mm10
Supplementary_files_format_and_content: .bw and .bed

source_name: bone marrow-derived macrophages

growth_protocol: bone marrow cells were isolated from femurs and tibias of adult mice and cultured for 5 days in a DMEM medium supplemented with M-CSF conditional medium

extract_protocol:
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against EZH2 ( Active Motif 39901).
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: non-treated (NT) or stimulated for 2 h with LPS

tag: agent

value: LPS

value: bone marrow

value: bone marrow-derived macrophages

tag: chip antibody

value: EZH2 (Active Motif, catalog# 39901, lot# 1)


title: BMDM input DNA

description: input


title: BMDM NT-EZH2_ChIPSeq

description: non-treated (NT)

value: control


title: WT_ABX_Jejunum_MM317-6


title: WT_ABX_Jejunum_MM317-7


title: KO_ABX_Jejunum_MM317-25

value: KO


title: KO_ABX_Jejunum_MM317-23


title: KO_ABX_Jejunum_MM317-22


title: KO_ABX_Jejunum_MM317-21


title: VPA 12w rep3

city: Ikoma

first: Taito

last: Matsuda

country: Japan

institute: Nara Institute of Science and Technology

data_processing:
RNA seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
Processed reads were mapped to the mouse genome mm10 genome using TopHat/Bowtie2.
Cuffdiff, a program in the Cufflinks software was used for differential gene expression analysis.
Genome_build: mm10

molecule: polyA RNA

source_name: Neural stem/progenitor cells

extract_protocol:
Forebrains or dentate gyrus were dissected from Nestin-EGFP mice and GFP-positive cells were isolated by FACS. mRNAs were isolated from the cells  for the construction of sequencing libraries using Dynabeads mRNA DIRECT Micro Kit (Invitrogen) following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Methylcellulose, as a control, or VPA (300mg/kg/day) was orally administered to pregnant Nestin-EGFP mice on E12, 13 and 14

value: Neural stem/progenitor cells

value: hippocampal dentate gyrus

tag: age

value: 12 weeks old

value: Nestin-EGFP


title: VPA 12w rep2


title: VPA+Run 12w rep2


title: VPA+Run 12w rep1


title: Control 12w rep3


title: KO BMDM LPS

description: LPS 2h

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: KO BMDM LPS

growth_protocol: bone marrow cells were isolated from femurs and tibias of adult WT and ezh2f/f lysmcre mice and cultured for 5 days in a DMEM medium supplemented with M-CSF conditional medium

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: KO BMDM NT

description: NT

source_name: KO BMDM NT


title: E7-5-A-IP-K27me3 rep2

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For Bisulfite seq, the trimmed reads were mapped to mm10 mouse genome following our modified bisulfite sequencing pipeline.(H Guo et al, Nature Protocol 10(5):645-59)
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: the bigwig files for ChIP-seq include the H3K27me3 modification in each sample with merged data from two biological replicates.

source_name: K27me3 microChIP

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; Genomic DNA acquired from ChIP assay (H3K27me3, merck millipore, catlog number: 07-449, lot number: 2275589) of embryo samples were separated and extracted by microChIP. Genomic DNA acquired from embryos were separated and extracted followed by bisulfite sequencing
Libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of single cell based bisulfite seq were constructed according to the protocol described in (H Guo et al, Nature Protocol 10(5):645-59).

value: ICR

value: 7.5 dpc

value: embryo

value: H3K27me3 (merck millipore, cat. 07-449, lot 2275589)


title: Control 12w rep1


title: WT BMDM NT

description: NT

source_name: WT BMDM NT

value: wild type


title: VPA P5 rep3

value: postnatal day5


title: VPA P5 rep1


title: Control P5 rep1


title: Control P5 rep3


title: VPA+Run 12w rep3


title: WT BMDM LPS

description: LPS 2h

source_name: WT BMDM LPS


title: Control 12w rep2


title: VPA E15 rep2

value: forebrain

value: embryonic day15


title: VPA E15 rep1


title: Control E15 rep2


title: Control E15 rep3


title: Control E15 rep1


title: VPA P5 rep2


title: VPA 12w rep1


title: WT_Jejunum_MM317-5

value: WT

value: NT


title: VPA E15 rep3


title: WT_Jejunum_MM317-4


title: WT_Jejunum_MM317-2


title: Control P5 rep2


title: KO_Jejunum_MM317-19


title: KO_Jejunum_MM317-18


title: KO_Jejunum_MM317-16


title: KO_Jejunum_MM317-17


title: WT_Colon_MM36

source_name: Colon


title: WT_Colon_MM33


title: KO_Colon_MM31


title: WT_Jejunum_MM27


title: KO_Colon_MM28


title: WT_Colon_MM30


title: WT_Jejunum_MM24


title: WT_Jejunum_MM21


title: KO_Jejunum_MM22


title: WT_Jejunum_MM317-3


title: KO_Jejunum_MM25


title: KO_Jejunum_MM19


title: WT_Ileum_MM15

source_name: Ileum


title: WT_Ileum_MM12


title: KO_Ileum_MM13


title: KO_Ileum_MM16


title: KO_Ileum_MM10


title: lmpp5-6

city: Boston

first: Soumya

last: Badrinath

state: MA

address: One Jimmy Fund Way

institute: Dana-Farber Cancer Institute

data_processing:
Drop-seq tools v1.12 (Macosko et al., 2015) for processing sequencing data (fastq files), specifying 10,000 or 20,000 cell barcodes to return for Drop-seq samples, or 100 or 200 cell barcodes for plate-sorting data
Fluorescent intensities (indices) of each antibodies were recorded and exported from the SONY SH800Z sorter as csv files, representing surface protein expression.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw UMI counts for each gene per cell.
Supplementary_files_format_and_content: mcluster.txt: Tab-delimited text file includes averaged expression count of micro-clusters (aggregates of 20 nearest neighbor cells).

organism: Homo sapiens

source_name: lmpp5_Cord blood

extract_protocol:
Drop-seq samples were prepared following the published protocols (Macosko et al., 2015). For single-cell index sorting samples, we followed a modified SMART-Seq2 protocol (Picelli et al., 2013), with the exception that a 12-base cell barcode was included in the 3’-end RT primer.
Libraries were prepared using the Nextera XT DNA sample prep kit (Illumina) using a custom Read 1 primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC, IDT).

treatment_protocol: Umbilical cord blood from anonymous healthy donors was obtained through the National Cord Blood Program from New York Blood Center. Within 48 hours after cord blood collection, mononuclear cells (MNCs) were isolated from each cord blood unit by density centrifugation using Ficoll-Paque PREMIUM (GE Healthcare #17-5442-03), and enriched for CD34+ cells using MACS separation (Miltenyi Biotec #130-100-453). Briefly, umbilical cord blood was diluted two folds using DPBS without calcium and magnesium (Corning #20-031-CV), layered on top of 15 ml Ficoll-Paque PREMIUM in a 50 ml Falcon tube, and spun down at 850 g for 30 min at room temperature with the brake off. The mononuclear cell layer was then isolated and washed with MACS buffer (DPBS with 0.5% BSA, Sigma-Aldrich #A8806-5G) after red blood cell lysing with ACK lysing buffer (Life Technologies #A10492-01). MNCs were then enriched for CD34+ cells by incubating them with magnetic beads conjugated to mouse anti-human CD34 antibody for 30 min, and passed through a magnetic MACS LS column (Miltenyi Biotec # 130-042-401). CD34+ cells would bind to the LS column and later flushed off and collected in 5 ml MACS buffer. For Drop-seq experiments, two consecutive enrichment steps were performed to increase the purity of enriched CD34+ cells.

tag: subject status

value: Healthy donor

value: hematopoetic stem and progenitor cells

tag: antibodies

value: CD34, CD38, CD45RA, CD10, SELL (CD62L), IL17RA


title: lmpp5-7


title: KO_Colon_MM34

value: KO


title: lmpp5-4


title: WT_Duodenum_MM9

source_name: Duodenum


title: WT_Duodenum_MM6


title: lmpp5-5


title: lmpp5-3


title: KO_Duodenum_MM7


title: KO_Duodenum_MM4


title: lmpp2-p9

source_name: lmpp2_Cord blood


title: lmpp5-1


title: WT_Ileum_MM18


title: lmpp2-p7


title: lmpp2-p6


title: Mast_45RApos

source_name: Mast_Cord blood

value: CD34, CD38, CD45RA, CD71, CD117, FceRI


title: lmpp2-p3


title: lmpp2-p4


title: NY6.1

source_name: NY6_Cord blood


title: KO_Duodenum_MM1


title: Mast_45RAneg


title: LIJ2.2

source_name: LIJ2_Cord blood


title: LIJ8.2

source_name: LIJ8_Cord blood


title: lmpp2-p5


title: ctrlhp_3

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
ATAC-seq was were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
bed-files including coordinates of the detected peaks from ATAC-seq.
Genome_build: Human hg38

source_name: Neural progenitor cells

growth_protocol: Differentiated human neural progenitor cell lines were used.

extract_protocol:
DNA was purified using Qiagen Qiaquick PCR purification kit and quantified using a Qubit Fluorometer according to the manufacturer’s instructions.
Libraries were prepared using previously published protocols (PMID: 25559105)

treatment_protocol: ATAC prococol was started 4 days after lentiviral infection.

value: Neural progenitor cells

tag: line

tag: Sex

value: F


title: ctrlhp_1


title: LIJ8.1


title: lmpp2-p2


title: WT_Duodenum_MM3


title: LIJ2.1


title: NY21.3

source_name: NY21_Cord blood


title: CLKhp_3


title: lmpp5-2


title: CLKhp_2


title: NY21.2


title: ctrlhp_2


title: NY21.1


title: AE6.3

source_name: AE6_Cord blood


title: X_3xOF4106_input

data_processing:
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
ChIP-seq data were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC).
ChIP-seq was analyzed using MACS2 with following parameter "--bw 300 --tsize 50 --nomodel --keep-dup all --extsize 300 -q 0.05 –nolambda".
ChIP-seq was analyzed using MACS2 with default parameter and "--nolambda --shift 75".
bed-files including coordinates of the detected peaks from ChIP-Seq.
Genome_build: Human hg38

growth_protocol: Differentiated human neural progenitor cells and adult human BA10 and BA40 neocortex was used

extract_protocol:
DNA was purified using Qiagen Qiaquick PCR purification kit, assayed for quality by Bioanalyzer (Agilent), and quantified using a Qubit Fluorometer according to the manufacturer’s instructions.
Libraries were prepared using previously published methods (PMID: 25662462)

treatment_protocol: 6μg of rabbit αCLOCK (ab3517, Abcam, lot #GR222742-4) was used for CLOCK ChIP and 6μg of normal rabbit αIgG (#2729, Cell Signaling) was used as a negative control. Please refer to manuscript for detailed ChIP protocol, adapted from Koike et. al. 2012 (PMID: 22936566).


title: X_3xOF4106_IgG


title: X_3x062409_input

value: M


title: X_3xOF4106_FLAG


title: ZT72.ctrl.2 (hi2500)

data_processing:
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (hg38, Gencode v.24). HiSeq 2500 and NextSeq 500 counts per gene were further added into a final count to calculate RPKM values and downstream analysis.
RNA-seq RPKM values were then quantified using in-home scripts, providing gene definitions (hg38, Gencode v.24).
Gene-level RPKMs quantifications were used for all downstream processing.
tab-delimited text file include RPKM values for each Sample.
Genome_build: Human hg38

extract_protocol:
Total RNA was extracted using Qiagen’s miRNeasy kit according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. 2ug of total RNA were enriched for mRNA with poly-A selection beads.  Libraries were prepared using previously published methods (PMID: 25662462)

treatment_protocol: Tissue culture was performed as previously described (PMID: 21647150). Lentivirus was delivered via pZIP shRNA constructs (Transomics).


title: ZT72.ctrl.1 (hi2500)


title: X_3x062409_FLAG


title: ZT72.CLKkd.2 (hi2500)


title: ZT72.CLKkd.3 (hi2500)


title: ZT72.ctrl.3 (hi2500)


title: BA40_1504_input

source_name: Brodmann area 40

value: Frozen brain tissue


title: ZT72.CLKkd.1 (hi2500)


title: ZT68.ctrl.3 (hi2500)


title: ZT68.ctrl.2 (hi2500)


title: BA40_1503_IgG


title: CLKhp_1


title: BA40_1504_IgG


title: BA40_1503_input


title: BA40_1502_input


title: ZT68.CLKkd.2 (hi2500)


title: BA40_1504_ab3517


title: ZT68.CLKkd.3 (hi2500)


title: BA40_1502_ab3517


title: ZT68.CLKkd.1 (hi2500)


title: AE6.2


title: BA40_1501_input


title: BA40_1501_IgG


title: BA40_1503_ab3517


title: ZT64.ctrl.1 (hi2500)


title: BA40_1500_input


title: ZT64.CLKkd.2 (hi2500)


title: X_3x062409_IgG


title: ZT64.CLKkd.3 (hi2500)


title: BA40_1501_ab3517


title: ZT64.CLKkd.1 (hi2500)


title: BA40_1500_ab3517


title: BA40_1500_IgG_S11


title: ZT68.ctrl.1 (hi2500)


title: ZT60.ctrl.2 (hi2500)


title: BA10_1504_input

source_name: Brodmann area 10


title: ZT60.ctrl.3 (hi2500)


title: BA40_1502_IgG


title: BA10_1504_ab3517


title: BA10_1504_IgG


title: BA10_1503_IgG


title: ZT60.CLKkd.3 (hi2500)


title: BA10_1503_input


title: ZT60.ctrl.1 (hi2500)


title: ZT60.CLKkd.1 (hi2500)


title: ZT60.CLKkd.2 (hi2500)


title: BA10_1503_ab3517


title: ZT64.ctrl.3 (hi2500)


title: ZT64.ctrl.2 (hi2500)


title: BA10_1502_input


title: ZT56.ctrl.3 (hi2500)


title: BA10_1502_IgG


title: ZT56.ctrl.1 (hi2500)


title: BA10_1502_ab3517


title: ZT56.ctrl.2 (hi2500)


title: ZT56.CLKkd.2 (hi2500)


title: ZT56.CLKkd.1 (hi2500)


title: BA10_1501_input


title: ZT52.ctrl.3 (hi2500)


title: BA10_1500_input


title: BA10_1500_IgG


title: ZT52.ctrl.1 (hi2500)


title: ZT52.CLKkd.3 (hi2500)


title: BA10_1500_ab3517


title: ZT72.ctrl.3 (ns500)


title: ZT52.CLKkd.2 (hi2500)


title: ZT52.ctrl.2 (hi2500)


title: ZT72.ctrl.1 (ns500)


title: ZT72.ctrl.2 (ns500)


title: ZT72.CLKkd.3 (ns500)


title: ZT48.ctrl.2 (hi2500)


title: ZT72.CLKkd.2 (ns500)


title: ZT48.CLKkd.3 (hi2500)


title: ZT72.CLKkd.1 (ns500)


title: ZT48.ctrl.3 (hi2500)


title: ZT48.CLKkd.2 (hi2500)


title: ZT48.CLKkd.1 (hi2500)


title: ZT56.CLKkd.3 (hi2500)


title: ZT68.ctrl.1 (ns500)


title: ZT48.ctrl.1 (hi2500)


title: ZT52.CLKkd.1 (hi2500)


title: ZT68.ctrl.2 (ns500)


title: BA10_1501_ab3517


title: ZT68.CLKkd.3 (ns500)


title: ZT44.ctrl.1 (hi2500)


title: BA10_1501_IgG


title: ZT44.CLKkd.3 (hi2500)


title: ZT64.ctrl.3 (ns500)


title: ZT64.ctrl.2 (ns500)


title: ZT44.CLKkd.1 (hi2500)


title: ZT44.CLKkd.2 (hi2500)


title: ZT68.ctrl.3 (ns500)


title: ZT64.CLKkd.3 (ns500)


title: ZT64.ctrl.1 (ns500)


title: ZT64.CLKkd.1 (ns500)


title: ZT60.ctrl.3 (ns500)


title: ZT40.ctrl.2 (hi2500)


title: ZT40.ctrl.1 (hi2500)


title: ZT40.CLKkd.3 (hi2500)


title: ZT60.CLKkd.2 (ns500)


title: ZT36.ctrl.2 (hi2500)


title: ZT60.CLKkd.3 (ns500)


title: ZT68.CLKkd.2 (ns500)


title: ZT64.CLKkd.2 (ns500)


title: ZT40.ctrl.3 (hi2500)


title: ZT44.ctrl.3 (hi2500)


title: ZT40.CLKkd.1 (hi2500)


title: ZT44.ctrl.2 (hi2500)


title: ZT60.ctrl.2 (ns500)


title: ZT36.ctrl.1 (hi2500)


title: ZT68.CLKkd.1 (ns500)


title: ZT36.CLKkd.3 (hi2500)


title: ZT60.CLKkd.1 (ns500)


title: ZT56.ctrl.3 (ns500)


title: ZT56.ctrl.2 (ns500)


title: ZT36.CLKkd.2 (hi2500)


title: ZT56.ctrl.1 (ns500)


title: ZT36.CLKkd.1 (hi2500)


title: ZT40.CLKkd.2 (hi2500)


title: ZT32.ctrl.2 (hi2500)


title: ZT56.CLKkd.2 (ns500)


title: ZT60.ctrl.1 (ns500)


title: ZT56.CLKkd.1 (ns500)


title: ZT32.ctrl.3 (hi2500)


title: ZT52.ctrl.3 (ns500)


title: ZT32.CLKkd.3 (hi2500)


title: ZT32.ctrl.1 (hi2500)


title: ZT32.CLKkd.2 (hi2500)


title: ZT32.CLKkd.1 (hi2500)


title: ZT52.ctrl.2 (ns500)


title: ZT28.ctrl.3 (hi2500)


title: ZT52.CLKkd.3 (ns500)


title: ZT28.ctrl.2 (hi2500)


title: ZT28.ctrl.1 (hi2500)


title: ZT52.CLKkd.1 (ns500)


title: ZT52.CLKkd.2 (ns500)


title: ZT36.ctrl.3 (hi2500)


title: ZT48.ctrl.2 (ns500)


title: ZT52.ctrl.1 (ns500)


title: ZT28.CLKkd.3 (hi2500)


title: ZT28.CLKkd.2 (hi2500)


title: ZT28.CLKkd.1 (hi2500)


title: ZT48.ctrl.3 (ns500)


title: ZT24.ctrl.3 (hi2500)


title: ZT48.CLKkd.3 (ns500)


title: ZT24.ctrl.2 (hi2500)


title: ZT48.ctrl.1 (ns500)


title: ZT56.CLKkd.3 (ns500)


title: ZT24.ctrl.1 (hi2500)


title: ZT48.CLKkd.1 (ns500)


title: ZT24.CLKkd.3 (hi2500)


title: ZT44.ctrl.3 (ns500)


title: ZT24.CLKkd.1 (hi2500)


title: ZT44.ctrl.2 (ns500)


title: ZT24.CLKkd.2 (hi2500)


title: ZT44.ctrl.1 (ns500)


title: ZT20.ctrl.3 (hi2500)


title: ZT20.ctrl.2 (hi2500)


title: ZT20.ctrl.1 (hi2500)


title: ZT40.ctrl.2 (ns500)


title: ZT40.ctrl.1 (ns500)


title: ZT44.CLKkd.2 (ns500)


title: ZT20.CLKkd.2 (hi2500)


title: ZT20.CLKkd.3 (hi2500)


title: ZT40.CLKkd.2 (ns500)


title: ZT40.CLKkd.3 (ns500)


title: ZT36.CLKkd.2 (ns500)


title: ZT36.ctrl.2 (ns500)


title: ZT36.ctrl.1 (ns500)


title: ZT40.ctrl.3 (ns500)


title: ZT32.ctrl.3 (ns500)


title: ZT36.CLKkd.1 (ns500)


title: ZT40.CLKkd.1 (ns500)


title: ZT32.ctrl.2 (ns500)


title: ZT32.ctrl.1 (ns500)


title: ZT48.CLKkd.2 (ns500)


title: ZT32.CLKkd.2 (ns500)


title: ZT32.CLKkd.1 (ns500)


title: ZT44.CLKkd.1 (ns500)


title: ZT28.ctrl.2 (ns500)


title: ZT28.ctrl.3 (ns500)


title: ZT32.CLKkd.3 (ns500)


title: ZT28.ctrl.1 (ns500)


title: ZT28.CLKkd.3 (ns500)


title: ZT24.ctrl.3 (ns500)


title: ZT24.ctrl.2 (ns500)


title: ZT20.CLKkd.1 (hi2500)


title: ZT24.CLKkd.2 (ns500)


title: ZT36.CLKkd.3 (ns500)


title: ZT24.CLKkd.3 (ns500)


title: ZT36.ctrl.3 (ns500)


title: ZT28.CLKkd.1 (ns500)


title: ZT20.ctrl.3 (ns500)


title: ZT20.ctrl.2 (ns500)


title: ZT20.ctrl.1 (ns500)


title: ZT20.CLKkd.3 (ns500)


title: ZT20.CLKkd.1 (ns500)


title: ZT20.CLKkd.2 (ns500)


title: HepG2_RNA_seq_shMETTL14_IP_rep2

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.4 with default parameters; then the processed reads were mapped to hg19 whole genome using TopHat v2.0.13 with default parameters
RPKM for each sample and log2 fold change were calculated by using cuffdiff v2.2.1
The different m6A level were were calculated by using exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and different m6A level genes

source_name: HepG2 cells

growth_protocol: The human hepatocellular carcinoma cell line HepG2 (ATCC HB-8065) was maintained in EMEM medium (ATCC) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 2 mM L-Glutamine and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kit (Zymo). mRNA was further purified using Dynabeads mRNA DIRECT Kit (Thermo Fisher). For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packing vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least two passages by adding 1 μg/mL puromycin into growth medium.

tag: shRNA

tag: ip antibody

value: m6A antibody (Synaptic Systems, 202003)


title: ZT24.CLKkd.1 (ns500)


title: HepG2_RNA_seq_shCont_IP_rep2

value: Non-specific control


title: HepG2_RNA_seq_shCont_input_rep2


title: HepG2_RNA_seq_shMETTL14_input_rep2


title: HepG2_shIGF2BP1_RNA-seq_rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.4 with default parameters;then the processed reads were mapped to hg19 whole genome using hisat2 v2.0.4 with default parameters.
Reads count was calculated by using HTSeq and was converted to RPKM by a custom script.
RKPM were converted to attomole by linear-fitting of the RNA spike-in.
half-life was calculated by using custom script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and mRNA half-life

growth_protocol: The human hepatocellular carcinoma cell line HepG2 (ATCC HB-8065) was maintained in EMEM medium (ATCC) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 2 mM L-Glutamine and 1% penicillin-streptomycin. Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packing vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least two passages by adding 1 μg/mL puromycin into growth medium.

extract_protocol:
The total RNA was extracted by miRNeasy Kit (Qiagen).
For RNA sequencing, equal amount of ERCC RNA spike-in control (Thermo Fisher Scientific) was added to the total RNA samples as internal controls before library construction. Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit.

treatment_protocol: HepG2 cells with stably expressed shRNAs against IGF2BPs or shNS were seeded into 6-well plates to get 50% confluency after 24 hours. Cells were then treated with 5 μg/mL actinomycin D and collected at indicated time points.

value: HepG2 cells

value: untreated

tag: time point


title: HepG2_shIGF2BP3_RNA-seq_rep3


title: HepG2_shIGF2BP2_RNA-seq_rep2


title: ZT28.CLKkd.2 (ns500)

tag: cell type


title: HepG2_shIGF2BP2_RNA-seq_rep3


title: HepG2_shIGF2BP2_RNA-seq_rep1


title: HepG2_shIGF2BP3_6h_rep2

value: 5 μg/mL actinomycin D


title: HepG2_shNS_RNA-seq_rep3

value: shNS (non-specific control)


title: HepG2_shIGF2BP3_6h_rep1


title: ZT24.ctrl.1 (ns500)


title: HepG2_shIGF2BP3_3h_rep1


title: HepG2_shIGF2BP3_1h_rep2


title: HepG2_shIGF2BP3_1h_rep1


title: HepG2_shIGF2BP3_0h_rep1 (RNA-seq_rep1)


title: HepG2_shIGF2BP1_6h_rep2


title: HepG2_shIGF2BP1_1h_rep2


title: HepG2_shIGF2BP1_3h_rep1


title: HepG2_shIGF2BP3_3h_rep2


title: HepG2_shIGF2BP1_6h_rep1


title: HepG2_shIGF2BP3_0h_rep2 (RNA-seq_rep2)


title: HepG2_shIGF2BP1_0h_rep1 (RNA-seq_rep1)


title: HepG2_shIGF2BP1_3h_rep2


title: HepG2_shIGF2BP1_1h_rep1


title: HepG2_shNS_3h_rep2


title: HepG2_shIGF2BP1_0h_rep2 (RNA-seq_rep2)


title: HepG2_shNS_6h_rep2


title: HepG2_shNS_3h_rep1


title: HepG2_shNS_1h_rep2


title: HepG2_shNS_1h_rep1


title: HepG2_RNA_seq_shMETTL14_input

description:
HepG2_RNA_seq_rpkm_filter02_and_geneName.txt
shM14_vs_shCont_con_sig_m6A_diff_gene_result.txt


title: HepG2_shNS_0h_rep2 (RNA-seq_rep2)


title: HepG2_shNS_0h_rep1 (RNA-seq_rep1)


title: E06: BEP, biol. repl. 2

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

data_processing:
trimming with Trimmomatic 0.36, single end mode, removing adapter sequences
alignment using STAR 2.5.3a, alignIntronMax 1
counting with featureCount from subread 1.5.3

organism: Streptococcus pneumoniae D39

source_name: BEP (blood, exponential phase)

growth_protocol: D39 was pre-cultured before innoculation in aforementioned liquid medium. After certain period, the cells were harvested for total RNA.

extract_protocol:
Total RNA were harvested following phenol-chloroform separation, gDNA digestion and alcohol precipitation
Library were prepared according to manufacturer's protocol (Illumina), keeping stranded information

tag: strain

value: cultured monoclonal bacteria


title: E05: BEP, biol. repl. 1


title: HepG2_RNA_seq_shCont_IP


title: IGF2BP3-Input

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.4 with default parameters.
1nt was removed from each end of all reads and masked for low-complexity or low-quality sequence by using cutadapt v1.9.1 with parameters -u 1 -u -1 -q 20,20.
then the processed reads were mapped to hg19 whole genome using TopHat v2.0.13 with default parameters
FPKM for each sample and log2 fold change were calculated by using cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: excel table include FPKM values for each Sample and log2 fold change for the paired samples

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in DMEM medium (Invitrogen) containing 10% FBS, 2 mM L-Glutamine and 1% penicillin-streptomycin.

extract_protocol:
When reaching a confluency of 70-80%, cells in 10 cm dishes were cross-linked by UV and harvested by trypsinization. Nuclear extraction was isolated and sonicated. One microgram of Flag (Sigma-Aldrich) antibody was conjugated to Protein A/G Magnetic Beads (Thermo Fisher Scientific) by incubation for 4 hours at 4 °C, followed by 3x wash and incubation with pre-cleared nuclear extraction in RIP buffer [150 mM KCl, 25 mM Tris (pH 7.4), 5 mM EDTA, 0.5 mM DTT, 0.5% NP40, 1x protease inhibitor] at 4 °C overnight. After washing with RIP buffer for three times, beads were resuspended in 80 μL PBS, followed by DNA digestion at 37 °C for 15 min and incubation with 50 μg of Proteinase K (Thermo Fisher) at 37 °C for 15 min. Input and co-immunoprecipitated RNAs were recovered by TRIzol (Invitrogen) extraction.
NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation, which used dUTP in cDNA synthesis to maintain strand specificity. In short, the immunoprecipitated RNAs were reverse transcribed to 1st strand cDNA, followed by 2nd strand cDNA synthesis labelled with dUTP. The purified cDNA was end repaired and dA tailed, and then ligated to adapter with a stem-loop structure. The dUTP-labelled 2nd strand cDNA was removed by USER enzyme to maintain strand specificity. After indexing via PCR (~12 cycles) enrichment, the amplified libraries together with library preparation negative control were cleaned up by AMPure XP beads for QC analysis. To check the quality and yield of the purified library, one microliter library was analyzed by Bioanalyzer (Agilent, Santa Clara, CA) using DNA high sensitivity chip.

treatment_protocol: 1x106 HEK293T cells were seeded in 6-well plate and transfected with 4 µg Flag-tagged IGF2BP1/2/3 plasmids using lipofectamine 2000 at 24 hours after plating. Cells were expanded into 10 cm cell culture dishes 24 hours after transfection.

tag: ectopicaly expressed protein

value: Flag-tagged IGF2BP3


title: E04: N2B, biol. repl. 2

source_name: N2B (nose-blood, 5min)


title: HepG2_RNA_seq_shCont_input


title: IGF2BP3-IP

tag: rip antibody

value: Monoclonal anti-Flag® M2 antibody (Sigma-Aldrich)


title: E03: N2B, biol. repl. 1

tag: tissue


title: HepG2_shNS_6h_rep1

tag: treatment


title: D12: N2F, biol. repl. 2

source_name: N2F (nose-CSF, 5min)


title: IGF2BP1-Input

value: Flag-tagged IGF2BP1


title: IGF2BP2-Input

value: Flag-tagged IGF2BP2


title: IGF2BP2-IP


title: IGF2BP1-IP


title: D11: N2F, biol. repl. 1


title: D08: FEP, biol. repl. 2

source_name: FEP (CSF, exponential phase)


title: D06: F40, biol. repl. 2


title: C08: LEP, biol. repl. 2

source_name: LEP (lung, exponential phase)


title: D04: B2C, biol. repl. 2

source_name: B2C (blood-C+Y, 5min)


title: D05: F40, biol. repl. 1


title: D07: FEP, biol. repl. 1


title: C07: LEP, biol. repl. 1


title: HepG2_RNA_seq_shMETTL14_IP


title: C02: N2L, biol. repl. 2

source_name: N2L (nose-lung, 5min)


title: B12: C20, biol. repl. 2

source_name: C20 (competence, 20min)


title: B11: C20, biol. repl. 1


title: B09: C10, biol. repl. 1

source_name: C10 (competence, 10min)


title: B08: C03, biol. repl. 2

source_name: C03 (competence, 3min)


title: C01: N2L, biol. repl. 1


title: B10: C10, biol. repl. 2


title: B07: C03, biol. repl. 1


title: A08: C2N, biol. repl. 2

source_name: C2N (C+Y medium-nose, 5min)


title: B05: CEP, biol. repl. 1

source_name: CEP (C+Y, exponential phase)


title: A09: NEP, biol. repl. 1

source_name: NEP (nose, exponential phase)


title: A07: C2N, biol. repl. 1


title: A04: ND6, biol. repl. 2

source_name: ND6 (nose-dessication, 60min)


title: A05: NDN, biol. repl. 1

source_name: NDN (nose-dessication, 5min-nose)


title: A06: NDN, biol. repl. 2


title: D03: B2C, biol. repl. 1


title: A03: ND6, biol. repl. 1


title: A02: ND5, biol. repl. 2

source_name: ND5 (nose-dessication, 5min)


title: Subject14_milk

status: Public on Mar 14 2018

first: Lorena

last: Pantano

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

data_processing:
An initial QC was conducted using FASTX-Toolkit and FastQ Screen. After adaptor removal, reads with the following features were removed: 1) Reads <18nt, 2) Mean PHRED scores < 30, and 3) Low complexity reads based on mean score of the read
Sequences fulfilling QC were used as the input of the seqBuster/seqCluster tool that retrieves three matrices of counts: i) miRNA, ii) isomiRs, and iii) small RNA clusters
In order to detect miRNAs and isomiRs, reads were mapped to hairpins released from miRBasev21 using miraligner
In parallel, sequences were mapped to hs37d5 using bowtie, and hotspots (sets of overlapping sequences according to their position in the genome) were detected
Hotspots sharing any sequence were grouped in primary clusters. Then, a recursively heuristic algorithm based on reduction and cluster correction was applied to the ones sharing over 60% of the sequences. These were annotated to different RNA species using miRBase v20, refGene (RefSeq genes), wgRna (CD and H/ACA Box snoRNAs and miRNAs from Weber and Griffiths-Jones), rmsk (Repeating elements created using RepeatMasker) and tRNA from University of California Santa Cruz (UCSC) genome browser (hg19), and piR_hg19_v1.0 from the regulatoryrna database (www.regulatoryrna.org).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of unnormalized counts per gene

source_name: Breast milk

extract_protocol:
Small RNAs were extracted using the miRNeasy Serum/Plasma kit (Qiagen, Cat No.: 217184) with minor modifications. RNA extraction was performed from at least 3 mL of plasma and milk. One mL of biofluid was filtered per each column and washed two times with ethanol 80% before elution
Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) (NEB, Cat No.: E7330) following manufactures instructions and using 150ng of RNA obtained from plasma samples and 500 ng from milk. Library size selection was done using acrylamide gels.

tag: age (years)

tag: region of origin

value: Asia

tag: parity

tag: rna concentration (ng/ml)


title: Subject13_milk

value: Spain


title: Subject12_milk


title: Subject08_milk

value: South America


title: Subject07_milk

value: Morroco


title: Subject09_milk


title: Subject10_milk


title: Subject03_milk


title: Subject04_milk


title: Subject07_plasma

source_name: Plasma


title: Subject14_plasma


title: Subject11_plasma


title: Subject08_plasma


title: Subject02_milk


title: B06: CEP, biol. repl. 2


title: Subject03_plasma


title: UVA-2

city: Chicago

first: Yu-Ying

last: He

state: IL

address: 5841 S Maryland Ave, AMB N011

department: Medicine

institute: University of Chicago

description: UVA-irradiated keratinocytes (20J/cm2)

data_processing:
Quality control analysis of raw data using FastQ Groomer v1.0.4
Read alignment using Tophat2
Transcript assembly using Cufflinks v2.2.1
Assemblies merged using CuffMerge v1.0.0
Differential gene expression analysis using CuffDiff v2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample from Cufflinks

source_name: Normal Human Epidermal Keratinocytes

growth_protocol: Adult normal human epidermal keratinocytes (NHEKs) obtained from Lonza (cat. #: 192627) were grown in KGM-Gold BulletKit medium (Lonza) according to manufacturer's protocol. Cells were cultured at 37°C and in 95% air/5% CO2 (vol/vol). Cells were passaged 3 times.

extract_protocol:
NHEKs were purified 6h after radiation using Qiagen Rneasy Plus kit according to manufacturer's instructions. RNA quality was assessed using Agilent Bioanalyzer.
An oligo dT-selected library was prepared and sequencing was performed on an Illumina HiSeq2000 platform with 50 bp single-end reads by the Functional Genomics Facility at the University of Chicago using standard Illumina protocols.

treatment_protocol: NHEKs were washed 2X in PBS, supplemented with Dulbecco's modified PBS (DPBS, 1X), then treated with sham or UVA irradiation (20J/cm2).

value: epidermis

tag: age

value: adult


title: Sham-1

description: Sham-irradiated keratinocytes


title: A10: NEP, biol. repl. 2


title: A01: ND5, biol. repl. 1


title: UVA-1

description: UVA-irradiated keratinocytes (20J/cm2)


title: Sham-2

description: Sham-irradiated keratinocytes


title: UC_inb66

city: Copenhagen N

first: Morana

last: Vitezic

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Basecalling was done by CASAVA version 1.8.2. The first 11 nt from 5'-end and the last 13nt from 3'-end are trimmed off resulting in 25 nucleotide reads.
CAGE tags were mapped using the Bowtie4 (version 0.12.7) (to the hg19 assembly using v=2 and otherwise standard settings but allowing for multiple alignments. Subsequently, only uniquely mapping reads were retained. Reads that mapped to unconventional chromosomes or chrM were discarded.
5’ ends of the CAGE tags that mapped close to each other on the same strand were grouped into tag clusters (TCs), To remove cluster tails before subsequent expression analysis a queue based trimming algorithm was applied to  all  clusters,  removing  tags from the ends until a maximum of 10 % of the total number of tags has been trimmed  away
Expression was calculated as Tags Per  Million  (TPM),  by counting  the  tags  per  TSS  and  normalizing  to  library  size  (tags/total  tags  in library*1e6). Unless otherwise mentioned, only TCs having 1 or more TPM in at least 3 libraries were retained for further analysis. Information on batches can be obtained from supplementay data of the manuscript (to be determined).
Genome_build: hg19
Supplementary_files_format_and_content: ctss bed files for CAGE defined transcription start sites for each fastq file as processed by our pipeline

source_name: descending colon pinch biopsy

extract_protocol:
The RNA was extracted using PureLink® RNA Mini Kit (Ambion™, Life Technologies) with freshly made lysis buffer containing 1% 2-mercaptoethanol (Sigma).
CAGE libraries were prepared according to doi:10.1038/nprot.2012.005 with an input of 1500 ng of total RNA as starting material. CAGE libraries were prepared individually, but prior to sequencing four CAGE libraries with different barcodes were pooled and applied to the same sequencing lane. To compensate for the low complexity in the 5’ends of the CAGE libraries, 30% Phi-X spike-ins were added to each sequencing lane, as recommended by Illumina.

treatment_protocol: The biopsies were immediately placed in RNAlater® Stabilization Solution (Ambion™, Life Technologies) and kept at 4°C for 24 hours before long term storage at -80 °C

value: colon

tag: condition

value: UC inactive

tag: barcode


title: UC_in39


title: UC_inb58


title: UC_inb03


title: UC_inb85


title: UC_inb79


title: UC_inb34


title: UC_inb13


title: UC_inb82


title: UC_inb20


title: UC_in30


title: UC_in28


title: UC_inb47


title: UC_in35


title: UC_inb05


title: UC_in21


title: UC_ab88

value: UC active


title: UC_ab90


title: UC_ab89


title: UC_ab92


title: UC_ab91


title: UC_ab86


title: UC_ab6


title: UC_ab56


title: UC_ab83


title: UC_ab80


title: UC_in40


title: UC_ab50


title: UC_ab7


title: UC_ab11


title: UC_a49


title: UC_a_b51


title: UC_a46


title: cont_b77

value: control


title: UC_a52


title: UC_ab84


title: UC_ab41


title: UC_a111


title: cont_b78


title: cont_b75


title: cont_b69


title: cont_b74


title: cont_b64


title: UC_ab59


title: cont_b62


title: UC_ab25


title: UC_a43


title: cont_b60


title: cont_b57


title: cont_b53


title: cont_b63


title: cont_b45


title: UC_a_b87


title: cont_b48


title: cont_b38


title: cont_b73


title: cont_b32


title: cont_b33


title: cont_b23


title: cont_8


title: cont_b18


title: cont_4


title: cont_b22


title: cont_b31


title: cont_14


title: cont_b16


title: cont_9_1


title: cont_15


title: cont_12


title: CD_in104

value: CD inactive


title: CD_in106


title: CD_a1957

value: CD active


title: CD_a1958


title: CD_a1954


title: CD_a1956


title: CD_in105


title: CD_a1955


title: CD_a1953


title: UC_ab10


title: cont_b54


title: CD_a1951


title: CD_a1950


title: CD_a1949


title: CD_a1947


title: CD_a1946


title: CD_a109


title: CD_a1945


title: CD_a103


title: CD_a110


title: CD_a108


title: CD_a102


title: k4m2_nILC2_1

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

data_processing:
Reads were aligned using bowtie2 (ChIPmentation) or HISAT (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
ChIPmentation: HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
RNA-seq: Sample scaling and statistical analysis were performed using the R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: HOMER peak calling (ChIPmentation) or RPKM expression values (RNA-Seq)

source_name: peripheral blood

growth_protocol: Only for aILC2: 7 days of culture (no feeders) in Yssel's medium supplemented with IL-2, IL-7, IL-25 and IL-33. See Lim et al. Journal of Experimental Medicine (2016)

extract_protocol:
Murine ILC2s were obtained from Gata3-YFP/YFP mice with airway inflammation, human ILC2s from peripheral blood. Cells were FACS-sorted using specific antibodies (and YFP for murine cells) as described in detail in the manuscript.
ChIPmentation: Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015); RNA-Seq: Smart-seq2library construction (as described in Picelli et al. Nature Methods (2013)

value: FACS-purified lymphocytes

tag: antibody

value: anti-H3K4Me2, Abcam ab32356


title: k4m2_nILC2_3


title: PC9

first: FAN

last: ZHANG

state: Shanghai

address: 507 Zhengmin Road

institute: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling. FASTQ files were generated,FASTQ files include the detailed read sequences and the read quality information.
Filter out “dirty” raw reads: 1) Remove reads with adaptors;2) Remove reads with unknown bases more than 5%;3) Remove low quality reads (which are defined as reads having more than 50% bases  with quality value ≤ 10).
The RNA-seq reads were aligned to the hg19 genome assembly using TopHat (version 1.1.4) with the default parameters
The expression index was generated using GFOLD V1.1.3 job count from the bam files from TopHat
The differentially expressed genes were ranked using GFOLD V1.1.3 job diff
The final output file contains all genes with a GFOLD value, which could be considered as the reliable log2-fold change between the control (PC9) and treatment (PC9R) conditions
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the GFOLD value (similar to the log2 fold change between two samples), RPKM, and other metrics for each gene ID
Supplementary_files_format_and_content: PC9_RNA_rep.read_cnt abundance measurements (txt format) this file contains the following information for each gene ID in the PC9 cells:read count, exon length, and RPKM
Supplementary_files_format_and_content: PC9R_RNA_rep.read_cnt abundance measurements (txt format) this file contains the following information for each gene ID in the PC9R cells:read count, exon length, and RPKM
Supplementary_files_format_and_content: PC9RvsPC9_rep.diff GFOLD output file (txt format) this file contains GFOLD output file with the following information for each gene ID:Gene Name,GFOLD(0.01),E-FDR, log2fdc, 1stRPKM(PC9R), 2ndRPKM(PC9)

source_name: Cell line

growth_protocol: PC9 and PC9R cells were grown in DMEM medium (Hyclone, GE Healthcare Life Sciences, Utah, USA).All medium contained 10% FBS (Gibco) supplemented with penicillin (100 U/ml) and streptomycin (100 mg/ml) (Life Technologies). In addition, gefitinib was added to the medium of the PC9R cells at a final concentration of 3 µM.

extract_protocol:
The total RNA was extracted from the PC9 and PC9R cells using RNAprep Pure (Tiangen, DP430, Shanghai, China), and the mRNAs were purified using the Dynabeads mRNA purification kit (Invitrogen, 61006).
The cDNAs were synthesized and used to construct a library with the NEBNext Ultra RNA Library Prep Kit (NEB, E7530).The libraries were sequenced on the Illumina HiSeq2000 platform via a 1x50bp single-end sequencing at BGI Tech Solutions Co., Ltd. (Shenzhen, China).

value: NSCLC cell

tag: cell line


title: 18773_WTBM-input_S1_L999_R1_001

city: Duarte

first: Juan

last: Du

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

data_processing:
ChIP-seq: Illumina Casava1.8 software used for basecalling. Reads were aligned to mouse reference genome (mm9) using NovoAlign (http://www.novocraft.com/).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Total bone marrow

extract_protocol:
ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following  previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248)  with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter).
ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.

treatment_protocol: Gene-trap knockout

tag: cell source

value: Total bone marrow

tag: genotype

value: WT

tag: ChIP

value: Input


title: 19181_JKO-HSPC-native-H4_L999_R1_001

source_name: stem/progenitor from bone marrow

value: stem/progenitor from bone marrow

value: JMJD1B knockout

value: Anti-H4, Abcam, Cat# Ab10158


title: k4m2_nILC2_2

tag: cell type


title: 18777_JKOBM-input_S5_L999_R1_001


title: 18774_WTBM-H3K9-1_S2_L999_R1_001

value: Anti-H3K9me2, Abcam, Cat#:Ab1220


title: 18780_JKOBM-H4R3_S8_L999_R1_001

value: Anti-H4R3me2s, Active Motif Cat#61187


title: 18778_JKOBM-H3K9-1_S6_L999_R1_001


title: 19180_JKO-HSPC-native-H3K9me2_L999_R1_001


title: 19176_WT-HSPC-native-H3K9me2_L999_R1_001


title: 19178_JKO-HSPC-native-input_S4_L999_R1_001


title: CD_a1948

value: colon


title: 19174_WT-HSPC-native-input_S7_L999_R1_001


title: 19175_WT-HSPC-native-H4R3me2s_L999_R1_001


title: 19172_JKO-BM-xlink-jmjd1B_S5_L999_R1_001

value: Anti-JMJD1B, Bethyl, Cat# A300-883A


title: 19177_WT-HSPC-native-H4_L999_R1_001


title: PC9R


title: CD_a107


title: 19171_JKO-BM-xlink-input_S4_L999_R1_001


title: BM_DN3_1percent_input-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

data_processing:
ChIP-Sequencing and data analysis: ChIP sequences were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory {Heinz, 2010 #67} for further downstream analysis. In addition, read alignments from the Scid.adh.2c2-PU.1ert2 experiment were filtered against PCR duplicates using Samtools as well as genomic repeats and Broad blacklisted regions using Bedtools (full script provided upon request) prior to tag directory generation. Transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score >= 15, were considered for further analysis.  Regions enriched for histone modifications were identified with findPeaks.pl with the option –style histone against a matched input control. Only regions consistently called in two independent experiments were used for downstream analyses.  Motif enrichment analysis was performed with the findMotifsGenome.pl command in the HOMER package using a 200bp window or a window size defined by the width of each identified peak. Overlapping peaks between samples were derived using mergePeaks.pl (default parameters). Annotation of peaks to genes and genomic regions (e.g. promoters, CG-rich regions, repeat regions) were performed with annotatePeaks.pl (default settings). Tag density plots and heat maps were created with annotatePeaks.pl ( –hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include HOMER IDR peaks. All genomic coordinates are relative to mm9 mouse assembly.

source_name: Lin- BM derived DN3 cells

extract_protocol:
Lin- BM isolation / culture protocolBone marrow (BM) was removed from the femur and tibia of 2-3 month-old Cas9 mice. Suspensions of BM cells were prepared and stained for lineage markers using biotin-conjugated lineage antibodies (CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, CD3ε, B220), then incubated with streptavidin-coated magnetic beads, and passed through a magnetic column. Lin− cells were eluted and cultured on OP9-DL1 monolayers using OP9 medium supplemented with 10 ng/ml of IL-7 and 10 ng/ml of Flt3L. On day 5, cultured cells were disaggregated, filtered through 40-μm nylon mesh and DN1 cells (Lin-, CD45+, Kit+,CD25-) were sorted. On day 14,DN3 ( Lin-CD45+Kit-CD25+) were harvested.
Ten million of BM-derived DN1 and DN3 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%. The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco). Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power. Five μg per 107 cells of anti-Runx1 Abs (ab23980,Abcam) were hybridized to Dynabeads M-280 Sheep anti-Rabbit IgG (Invitrogen) and added to the diluted chromatin complex. They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.
ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.

tag: strain

value: bone marrow

value: Cultured on OP9DL1

tag: chip antibody

value: none (input)


title: 19169_WT-BM-xlink-jmjd1b_S2_L999_R1_001


title: 18776_WTBM-H4R3_S4_L999_R1_001


title: BM_DN3_aRunx1-ChIP-rep1

tag: tissue

value: anti-Runx1 Abs (ab23980,Abcam)


title: BM_DN3_1percent_input-rep1

tag: treatment


title: BM_DN1_1percent_input-rep2

source_name: Lin- BM derived DN1 cells


title: BM_DN1_aRunx1-ChIP-rep2


title: BM_DN1_1percent_input-rep1


title: BM_DN1_aRunx1-ChIP-rep1


title: 19179_JKO-HSPC-native-H4R3me2s_L999_R1_001


title: E13.5WL_4_14

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description:
Single-cell_RNA-seq_Gene_Read_Count.txt.gz
Single-cell_RNA-seq_Gene_RPKM.txt.gz

data_processing:
The sequencing reads were aligned to the Mus musculus genome (mm10) using TopHat (v2.1.0) with the parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
Reads aligned to genes were counted using HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
Gene expression levels were quantified as reads per kilobase of the longest transcript per million mapped reads (RPKM).
genome build: mm10
processed data files format and content: values tab-delimited text files include read count and RPKM values for each sample

source_name: Pancreas

extract_protocol:
cDNA synthesis was performed following the Smart-seq2 method described by Picelli et al. 0.1 ul ERCC spike-in RNA (1:1,000,000 dilution, Life, 4456740) was added to the 4 ul lysis buffer in single cell RNA-seq.
2.5 ng of cDNA was used to conduct library using “TruePrep DNA Library Prep Kit” (Vazyme, TD502).

tag: embryonic day

value: dorsal pancreas; E13.5 WT; Ngn3-low


title: E13.5WL_4_13


title: E13.5WL_4_11


title: E13.5WL_4_12


title: E13.5WL_4_04


title: E13.5WL_4_02


title: CD_a1952

value: CD active


title: E13.5WL_4_09


title: 19170_WT-BM-xlink-prmt5_S3_L999_R1_001

value: Anti-PRMT5, Millipore, Cat# 07-405


title: E13.5WL_4_07


title: E13.5WL_4_06


title: E13.5WL_3_07


title: E13.5WL_4_08


title: E13.5WL_4_05


title: E13.5WL_4_03


title: BM_DN3_aRunx1-ChIP-rep2


title: E13.5WL_4_01


title: E13.5WL_3_04


title: 19168_WT-BM-xlink-input_S1_L999_R1_001

value: Total bone marrow


title: E13.5WL_3_05


title: E13.5WL_3_03


title: E13.5WL_3_02


title: E13.5WL_2_13


title: E13.5WL_3_01


title: E13.5WL_2_11


title: E13.5WL_2_12


title: E13.5WL_4_10


title: E13.5WL_2_09


title: E13.5WL_2_07


title: E13.5WL_2_06


title: E13.5WL_2_08


title: E13.5WL_2_05


title: E13.5WL_2_03


title: E13.5WL_2_02


title: E13.5WL_2_04


title: E13.5WL_2_01


title: E13.5WL_3_06


title: E13.5WL_2_10


title: E13.5KL_2_26

value: dorsal pancreas; E13.5 Pdx1-Cre; Jmjd3 fl/fl ; Ngn3-low


title: E13.5KL_2_31


title: E13.5KL_2_34


title: E13.5KL_2_32


title: E13.5KL_2_28


title: E13.5KL_2_25


title: E13.5KL_2_24


title: E13.5KL_2_18


title: E13.5KL_2_29


title: E13.5KL_2_17


title: E13.5KL_2_16


title: E13.5KL_2_30


title: E13.5KL_2_27


title: E13.5KL_2_33


title: E13.5KL_2_14


title: E13.5KL_2_15


title: E13.5KL_2_36


title: E13.5KL_2_35


title: E13.5KL_2_19


title: E13.5KL_2_13


title: E13.5KL_2_23


title: E13.5KL_2_20


title: E13.5KL_2_21


title: E13.5KL_2_22


title: E13.5KL_2_12


title: E13.5KL_2_09


title: E13.5KL_2_10


title: E13.5KL_2_08


title: E13.5KL_2_07


title: E13.5KL_1_18


title: E13.5KL_2_06


title: E13.5KL_2_04


title: E13.5KL_1_17


title: E13.5KL_1_16


title: E13.5KL_2_05


title: E13.5KL_2_01


title: E13.5KL_1_15


title: E13.5KL_1_13


title: E13.5KL_1_10


title: E13.5KL_1_09


title: E13.5KL_1_05


title: E13.5KL_1_07


title: E13.5KL_1_01


title: E13.5KL_1_08


title: E13.5KL_2_03


title: E13.5KL_2_11


title: E13.5WL_1_10


title: E13.5KL_1_14


title: E13.5KL_2_02


title: E13.5KL_1_11


title: E13.5WL_1_08


title: E13.5KL_1_12


title: E13.5WL_1_09


title: E13.5WL_1_06


title: E13.5WL_1_07


title: E13.5KL_1_06


title: E13.5KL_1_02


title: E13.5KL_1_03


title: E13.5KL_1_04


title: E13.5WL_1_05


title: E13.5WL_1_02


title: E13.5WL_1_03


title: E13.5WL_1_04


title: Input Ins1-positive #1

data_processing:
The sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters, and we only retained reads with a mapping quality ≥ 30 for subsequent analyses.
PCR duplicate reads were removed using samtools (v1.3.1) with the commands “samtools sort in_bam | samtools rmdup -s - out_bam”.
Reads of two biological replicates were pooled.
Tag density was calculated and stored in the bedGraph format using Homer with the parameters “makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20”.
genome build: mm10
processed data files format and content: bedGraph files were generated using Homer (v4.7.2); Scores represent read count per bp per 1 × 10e7 reads.

extract_protocol:
Low-cell-number ChIP-seq followed the method described by Brind'Amour et al. We used approximately 1.5 × 10e4 cells per ChIP with 1 ng antibodies of H3K4me3 (Abcam, ab8580), H3K27me3 (Millipore, 07-449), H3K4me1 (Millipore, 07-436), H3K27ac (Active motif, 39133), respectively.
Library preparation was conducted with “Ultra DNA Library Prep Kit for Illumina” (NEB. E7370).

value: E17.5 Ins1-RFP+


title: E13.5WL_1_01


title: NeuroD1 E14.5 #1

extract_protocol:
NeuroD1 ChIP-seq was performed following the method of Johnson et al. We used approximately 8 × 10e6 cells per ChIP with an antibody against NeuroD1 (Santa Cruz Biotechnology, sc-1084).
Library preparation was conducted with “Ultra DNA Library Prep Kit for Illumina” (NEB. E7370).

value: E14.5 whole pancreas


title: Input Ins1-positive #2


title: H3K4me3 Ins1-positive #1

value: H3K4me3 (Abcam, ab8580)


title: H3K27me3 Ins1-positive #2

value: H3K27me3 (Millipore, 07-449)


title: E17.5 Ins1-positive #2

description:
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_RPKM.txt.gz

data_processing:
The sequencing reads were aligned to the Mus musculus genome (mm10) using TopHat (v2.1.0) with the parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2”.
Reads aligned to genes were counted using HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf”.
Reads of two biological replicates were pooled.
Gene expression levels were quantified as reads per kilobase of the longest transcript per million mapped reads (RPKM).
The normalization of RPKM was performed by size factors which were calculated by function “estimateSizeFactorsForMatrix” of R package DESeq (v1.20.0).
genome build: mm10
processed data files format and content: values tab-delimited text files include read count and RPKM values for each sample

extract_protocol:
Total RNA were isolated from about 4-6 X 10e4 sorted cells by RNeasy Micro Kit (Qiagen, 74004). mRNA was purified from ~200 ng of total RNA by “NEBNext Poly(A) mRNA Magnetic Isolation Module” (NEB #E7490).
Libraries were prepared using” NEBNext Ultr Directional RNA Library Prep Kit for Illumina” (NEB #E7420) following the manufacturer’s instructions.


title: H3K4me1 Ins1-positive #1

value: H3K4me1 (Millipore, 07-436)


title: H3K27ac Ins1-positive #1

value: H3K27ac (Active motif, 39133)


title: H3K27ac Ins1-positive #2


title: H3K4me1 Ins1-positive #2


title: RNA_JKO1_R1

data_processing:
ChIP-seq: Illumina Casava1.8 software used for basecalling. Reads were aligned to mouse reference genome (mm9) using NovoAlign (http://www.novocraft.com/).
RNA-seq: Illumina Casava1.8 software used for basecalling. RNA-seq reads were aligned to the mouse reference genome (mm9) using TopHat2 . Gene expression abundance was quantified by reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bedGraph files with aligned and processed read coverage for each sample
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each sample

source_name: hematopoietic stem/progenitor cells from bone marrow

extract_protocol:
RNA: Total RNA is extracted using the Qiagen Rneasy micro kit. ChIP: ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following  previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248)  with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter).
ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.

tag: strainn


title: RNA_WT2_R1

value: wild type


title: JKO4-H4R3ME2S

value: ChIP grade anti-H4R3me2s (Abcam 5823)


title: JKO4-H3K9ME2

value: bone marrow

value: ChIP grade anti-H3K9me2 (Active Motif 39375)


title: RNA_WT1_R1


title: JKO3-H3K9ME2


title: H3K27me3 Ins1-positive #1


title: RNA_JKO2_R1


title: JKO3-H4R3ME2S


title: JKO4-INPUT

value: input


title: Input E14.5 #1


title: JKO3-INPUT


title: WT3-H3K9ME2


title: WT4-H3K9ME2


title: WT4-INPUT


title: WT4-H4R3ME2S


title: E17.5 Ins1-positive #1


title: WT3-INPUT


title: clt_2_CF_sedentary

city: Rochester

first: Eric

last: Small

state: NY

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

description: sedentary

data_processing:
Illumina bcltofastq v1.8.4 software used data formatting and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using SHRiMP v2.2.3 with the following parameters: -qv-offset 33 --all-contigs
The FASTX toolkit (fastq_quality_trimmer) was applied to remove bases with quality scores below Q=13 from the end of each read
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Differential expression analysis was performed using cufflinks v2.0.2; cufdiff2 with the following parameters: --FDR 0.05 -u -b $GENOME
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
polyA + mRNA was extracted from heart cells using Qiagen RNEasyPlus kit.
Stranded RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cardiac fibroblast

value: post natal week 10-14

tag: gender

value: male

value: sedentary


title: clt_20130813_2_CF_5d_MI

description: 5 day MI

value: 5 day MI


title: clt_L1_CF_4

description: 4 day swim

value: 4 day swim


title: clt_2_CM_sedentary

description: sedentary

value: Cardiomyocytes


title: clt_20130808_wt_CF

description: sedentary


title: clt_20130808_wt_CM

description: sedentary


title: clt_R1_CF_4

description: 4 day swim


title: clt_1_CF_sedentary

description: sedentary


title: clt_NT_CF_4

description: 4 day swim


title: clt_20130813_1_CF_5d_MI

description: 5 day MI


title: clt_R3_CF_10

description: 10 day swim

value: 10 day swim


title: clt_R1_CF

description: 3 day TAC

value: 3 day TAC


title: clt_NT_CF_3d_sham

description: 3 day TAC sham

value: 3 day TAC sham


title: clt_R2_CF

description: 3 day TAC


title: clt_3_CF

description: 10 day TAC

value: 10 day TAC


title: clt_L1_CF_3d_sham

description: 3 day TAC sham


title: clt_R1L2_CF_10_

description: 10 day swim


title: clt_L2_CF_10_

description: 10 day swim


title: WT3-H4R3ME2S


title: clt_L1_CF

description: 3 day TAC


title: clt_6_CF

description: 10 day TAC


title: Input Ngn3-high #2

value: dorsal pancreas; Ngn3-high


title: Input Ngn3-low #1

value: dorsal pancreas; Ngn3-low


title: H3K4me3 Ngn3-high #2

value: H3K4me3 (Abcam, ab8580)


title: H3K4me3 Ngn3-low #2


title: clt_1_CM_sedentary

description: sedentary

value: wild type


title: H3K4me1 Ngn3-high #2

value: H3K4me1 (Millipore, 07-436)


title: H3K4me3 Ngn3-low #1


title: H3K4me3 Ngn3-high #1


title: H3K27me3 Ngn3-high #2

value: H3K27me3 (Millipore, 07-449)


title: H3K4me1 Ngn3-high #1


title: H3K27me3 Ngn3-low #1


title: H3K27me3 Ngn3-high #1


title: H3K27me3 Ngn3-low #2


title: H3K4me1 Ngn3-low #2


title: Input Ngn3-low #2


title: clt_2_CF

description: 10 day TAC

value: Cardiac fibroblast


title: H3K27ac Ngn3-low #1

value: H3K27ac (Active motif, 39133)


title: H3K27ac Ngn3-high #1


title: H3K27ac Ngn3-low #2


title: Input Ngn3-high #1


title: 20_wildtype_H3K27ac

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
bcl2fastq version: 2.17.1.14 was used to convert RTA files generated from a Hiseq2000 run to Fastq files.
STAR 2.5.2b was used to align sequences to the mouse genome with parameters  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignIntronMax 1 --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
Picard Tools 2.7.1 markDuplicates was performed with standard settings to remove duplicate reads
Deeptools 2.4.0 bamCoverage was used to generate bigWig files with parameters --normalizeTo1x (mm10 genome size) --normalizeUsingRPKM -e -bs 10 --smoothLength 50
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files containing coverage information for ChIP and input DNA samples respectively.

source_name: wild type_H3K27ac

growth_protocol: A myleoid lineage specific constitutive knockout mouse line was generated by crossing Hdac1-2lox, Hdac2-2lox and Cx3cr1-Cre mice.

extract_protocol:
Mice were sacrificed at an age of 6 weeks and microglia were isolated by FACS sorting of brain homogenate for CD11bhi CD45lo cells.
Sequencing library preparation was performed using the KAPA Library Preparation Kit with Real-time PCR Library Amplification for Illumina Platforms Kit (Kapa Biosystems) as per the manufacturer’s protocol.

treatment_protocol: no treatment prior to FACS sorting

tag: strain background

tag: genotype/variation

value: FACS sorted microglia

tag: chip antibody vendor

value: active motif

tag: chip antibody cat. #

tag: chip antibody lot #


title: 22_wildtype_H3K27ac


title: 25_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K27ac


title: 23_wildtype_Input

source_name: wild type_Input

value: none (input DNA)


title: 21_wildtype_Input


title: H3K4me1 Ngn3-low #1


title: H3K27ac Ngn3-high #2


title: 18_wildtype_H3K9ac

source_name: wild type_H3K9ac

value: abcam


title: 12_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K9ac


title: 13_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_Input


title: 19_wildtype_Input


title: 17_wildtype_Input


title: 16_wildtype_H3K9ac


title: 15_wildtype_Input


title: 10_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K9ac


title: E13.5 Ngn3-high #1


title: E13.5 Ngn3-low #1


title: shSmyd5_CC_DNA-Seq

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

data_processing:
Library strategy: DNA-Seq
Basecalls performed using GAPipeline or CASAVA.
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate bedGraph files.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: bedGraph

source_name: Cancer cells, shSmyd5

growth_protocol: shLuc ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
gDNA was extracted from shLuc ESCs and shSmyd5 cancer cells using a Genomic DNA Purification kit from Promega, and sheared using a Diagenode bioruptor.
DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix.

value: cancer cells (CCs)

tag: shRNA


title: 11_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_Input


title: 09_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K27ac


title: shLuc_ESC_DNA-Seq

source_name: ESCs, shLuc

value: embryonic stem cells (ESCs)

value: shLuc


title: E13.5 Ngn3-low #2


title: E13.5 Ngn3-high #2


title: 14_wildtype_H3K9ac


title: mRNA_ILC2_MLN2

source_name: mediastinal lymph node (MLN)

value: FACS-purified lymphocytes


title: 26_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K27ac


title: mRNA_ILC2_BAL2

source_name: bronchoalveolar lavage (BAL)


title: mRNA_ILC2_MLN1


title: k4m2_ILC2_MLN2

tag: antibody

value: anti-H3K4Me2, Abcam ab32356


title: k4m2_ILC2_MLN1


title: k4m2_ILC2_BAL1


title: k4m2_ILC2_BAL2


title: E7.15_p2

city: Munich

first: Ilaria

last: Lavagi

address: Feodor Lynen Strasse 25

institute: Ludwid Maximilian University

data_processing:
SCRB-Seq libraries were demultiplexed from Nextera barcodes and cell barcodes
Alignments were calculated using STAR 2.5.2b using all default Parameters.
UMI tables were generated using the published Drop-seq pipeline (Macosko et al., 2015. Cell 161, 1202-1214)
Genome_build: Bos tau7 (NCBI) and ERCC spike-in reference
Supplementary_files_format_and_content: The 'umi_bosTau_ERCC.txt' contains the endogenous and ERCC UMI counts. These count has been performed after running Drop-seqAll reads were mapped to Bos tau7 (NCBI) and ERCC spike-in reference. Alignments were calculated using STAR 2.5.2b using all default parameters. UMI tables were generated using the published Drop-seq pipeline.
Supplementary_files_format_and_content: The normalized_UMI.txt:  Data were then normalized in the following way, to account for differences in efficiency of transcript recovery between wells: UMI counts were divided by the total number of UMI counts per cell and then multiplied by the median of total UMI counts across all cells.

organism: Bos taurus

source_name: Day3_16-cell stage

growth_protocol: Embryos were produced in vitro according to a standard procedure including in vitro maturation (IVM) and fertilization (IVF) (Reichenbach et al., 2010, Transgenic Research 19, 549-556). Briefly, follicles from slaughterhouse ovaries were aspirated and obtained cumulus-oocyte- complexes (COCs) matured for 23 h in MPM supplemented with LH and FSH and 5% estrous cow serum (ECS). Matured COCs were co-incubated with frozen-thawed sperm, prepared by the swim-up method. For IVM and IVF, COCs were incubated at 39°C in a maximum humidified atmosphere of 5% CO 2 in air. After 20 h of co-incubation, presumptive zygotes were vortexed to remove remaining cumulus cells and transferred to synthetic Oviductal fluid (SOF) supplemented with 5% ECS, 400 μl BME, 100 μl MEM under mineral oil and cultured at 5% CO 2 , 5% O 2 , 90% N 2 and 39°C in humidified air.

extract_protocol:
The zona pellucida was removed by treatment with 5 mg/ml pronase for 1 min. nzyme reaction was stopped by washing embryos in THP supplemented with 10% fetal calf serum (FCS) and dissolved ZP was completely removed by gentle pipetting. Embryos were incubated in drops of PBS without Mg 2+ and Cl 2+ supplemented with 4 mg/ml polyvinylpyrrolidone under oil for 5-10 min and blastomeres were subsequently disaggregated by gentle pipetting (Simmet et al., 2015). Single cells were transferred individually to 0.5 μl drops of Buffer A under mineral oil (Prelude Direct Lysis Module, NuGEN), collected in a 384-well plate and stored at -80 °C
Single Cell RNA Barcoding and Sequencing (SCRB-Seq) libraries were prepared (Soumillon et al., 2014). Briefly, the plate was thawed and 0.1 μl (1:10 6) ERCC RNA Spike-In Mix (Life Technologies) was added to each well; the addition of exogenous molecules in equal amount enabled us to later perform quality control. Cell barcode are reported in section “samples”.
Subsequently, the construct, which contains cell barcodes (6 nt), the Unique Molecular Identifiers (UMIs; 10 nt) and a polyT with the anchor, was incorporated to the sequence through the template switching reaction while RNA was reverse transcribed; Maxima H Minus Reverse Transcriptase (Thermo Scientific) was used. After this step, the samples were pooled. Not-incorporated barcode primers were removed through digestion with Exonuclease I (New England Biolabs). Full-length cDNA amplification was performed with the KAPA HiFi HotStart polymerase (KAPA Biosystems). Nextera XT libraries were constructed from 1 ng of pre-amplified cDNA with a custom P5 primer (IDT). The libraries were sequenced paired-end with 16 cycles to decode cell barcodes and UMI from read 1 and 45 cycles into the cDNA fragment.

tag: developemental stage

value: 16-cell stage

tag: embryo source

tag: cell barcode

value: GCACGG


title: E7.16_p2

value: GCCCTC


title: E7.14_p2

value: GAGCGG


title: E7.12_p2

value: CTGCGG


title: E7.13_p2

value: GACCGC


title: E7.8_p2

value: CGGCCA


title: E7.7_p2

value: CGCTGC


title: E7.5_p2

value: CGCCCT


title: E7.6_p2

value: CGCGCA


title: E7.3_p2

value: CCTGGC


title: E7.4_p2

value: CGAGGC


title: E7.10_p2

value: CGGTGG


title: E7.11_p2

value: CGTGGG


title: E6.16_p2

value: CCCTGG


title: E6.15_p2

value: CCCCGT


title: E6.14_p2

value: CCCACG


title: E6.11_p2

value: 16-cell stage

value: AGGGGC


title: E6.12_p2

value: CACGGC


title: E7.1_p2

value: CCGGAC


title: E6.10_p2

value: AGCGGG


title: mRNA_ILC2_BAL1

tag: cell type

value: FACS-purified lymphocytes


title: E6.13_p2

value: CAGGGG


title: Bone marrow-derived macrophages unstimulated control 3

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) toaccount for spliced reads alignments, allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.

source_name: Bone marrow

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines. Bone marrow-derived macrophages were collected from the femoral shafts and incubated in 100 mm x 15 mm petri dishes (Thermo Fisher Scientific) for 8 days in DMEM supplemented with 10% FCS, and 10% penicillin-streptomycin plus 30 ng/ml of M-CSF (Miltenyi Biotec, Bergisch Gladbach, GE). Following incubation, non-adherent cells were eliminated and adherent macrophages were scraped, counted and seeded in 6-well tissue-culture plates for stimulation at a density of 106 cells /ml.

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel, Düren, GE)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)

treatment_protocol: Macrophages were stimulated with Borrelia burgdorferi strain 297 at a multiplicity of infection of 25.

value: Bone marrow-derived macrophages

tag: strain

tag: age

value: 8 weeks

value: Non treated


title: E6.9_p2

value: ACGGGG


title: E6.8_p2

value: ACCGGC


title: Bone marrow-derived macrophages unstimulated control 2

tag: treatment


title: Bone marrow-derived macrophages Bb-stimulated 2

value: Stimulated with Borrelia burgdorferi 297


title: Bone marrow-derived macrophages Bb-stimulated 3


title: E6.7_p2

value: GTACCG


title: E7.9_p2

value: CGGGCT


title: E6.6_p2

value: CCAACC


title: E6.5_p2

value: TCTGCA


title: Bone marrow-derived macrophages Bb-stimulated 1


title: E6.4_p2

value: 16-cell stage

value: GTTCGA


title: E7.2_p2

value: CCGTCG


title: E6.2_p2

value: GCTAGA


title: Untreated rep3

first: Gottfried

last: Martin

address: Killianstr. 5

department: Klinik für Augenheilkunde

institute: Universitätsklinikum Freiburg

data_processing:
Read mapping: STAR 2.5.2b
Feature counting: featureCount from Subread 1.5.1 for R
Genome_build: mm11
Supplementary_files_format_and_content: tab delimited file containing gene symbols and reads for every sample

source_name: Retina

growth_protocol: 12 weeks old C57BL/6J mice were used. They were housed at 24 °C with a 12 h light / dark rhythm.

extract_protocol:
RNA was isolated from the retinas with the RNeasy kit (Qiagen, Hilden, Germany).
Library preparation and RNAseq were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina HiSeq 1000 System User Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA). In brief, 300 ng of total RNA was used for purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented to an average insert size of 200-400 bases using divalent cations under elevated temperature (94 °C for 4 min). The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification, because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Strand Synthesis Act D mix (FSA) prevents spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis, improving strand specificity. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final cDNA library. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.

treatment_protocol: During anesthesia with a mixture of 100 mg ketamine and 5 mg xylazine /kg, mice were injected i. p. with 200 mg/kg of a 100 mg/ml solution of eosin Y in 0.9 % NaCl to enhance the laser effect. The settings of the laser (Visulas 532s, Carl Zeiss Meditec, Jena, Germany) were 50 mW, spot size of 50 µm, 2.5 s duration. 3 - 6 laser applications were necessary to funduscopically occlude a vein. All veins of one eye of each mouse were occluded while the other eye served as control receiving the same laser application scheme (number of laser sites, intensity, and distance from the papilla) in retinal areas between the large vessels.

tag: tissue

value: retina

value: no laser treatment


title: E6.3_p2

value: GGGATT


title: E6.1_p2

value: CTAGTG


title: Untreated rep2


title: Control rep2

value: laser treatment between vessels


title: Control rep3


title: E13.14_p3

value: CCACAT


title: E13.12_p3

value: AGACCT


title: RVO rep3

value: laser treatment of all veins


title: Control rep1


title: RVO rep2


title: E13.11_p3

value: TTTTGA


title: RVO rep1


title: Bone marrow-derived macrophages unstimulated control 1

value: Bone marrow-derived macrophages

value: 8 weeks

value: Non treated


title: E13.10_p3

value: TTTCTT


title: E13.9_p3

value: 16-cell stage

value: TTTACA


title: E13.8_p3

value: TTGAAA


title: inducible_ko_control_P0_No_55

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M10) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_Matrix.txt").

source_name: FACS sorted Microglia

growth_protocol: All animals were maintained in SPF condition

extract_protocol:
Embryos and P0 pups were killed by decapitation. Other animals were killed by transcardial perfusion in anasthesia. Microglia cells were isolated from the brain by FACS sorting. Total RNA was extracted from sorted microglia by Pico Pure RNA extraction kit (Life Technologies) according to manufacturer’s protocol.
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: For constituitive knockout mice and controls no treatment prior to cell isolation was performed. For Tamoxifen induction in inducible knockout animals and controls Pregnant females were injected with 3 mg Tamoxifen (20 mg/ml Tamoxifen + 10 mg/ml Progesterone; Sigma‐Aldrich) intra peritonially at E13 to induce Hdac1 and 2 knock out at embryonic stage.

tag: genotype

value: Tamoxifen

value: neonatal


title: inducible_ko_control_P0_No_56


title: E13.6_p3

value: TTAGTT


title: E13.7_p3

value: TTATTG


title: inducible_ko_P0_No_57

value: HDAC1/2-loxP/loxP CX3CR1-CreERT2


title: Untreated rep1

value: retina

value: no laser treatment


title: inducible_ko_control_P0_No_54


title: inducible_ko_P0_No_53


title: E13.5_p3

value: TTAATC


title: E13.4_p3

value: TGTTTA


title: inducible_ko_P0_No_49


title: E13.13_p3

value: CACCAA


title: E13.3_p3

value: TGATTT


title: inducible_ko_P0_No_48


title: E13.2_p3

value: TCTTAA


title: E13.1_p3

value: TCATAT


title: inducible_ko_E16_No_8

value: embryonic day 16


title: inducible_ko_control_E16_No_5


title: inducible_ko_control_E16_No_6


title: inducible_ko_control_E16_No_4


title: E6.15_p3

value: 16-cell stage

value: TATAGA


title: E6.17_p3

value: TATTGT


title: E6.16_p3

value: TATGAA


title: inducible_ko_E16_No_3

value: Tamoxifen


title: E6.14_p3

value: TAGTAA


title: E6.13_p3

value: TACTAT


title: inducible_ko_control_E16_No_2


title: E6.12_p3

value: TAATGA


title: inducible_ko_6_wk_No_9

value: HDAC1/2-loxP/loxP CX3CR1-CreERT2

value: 45 days


title: E6.11_p3

value: TAAAGT


title: E6.8_p3

value: GATAAT


title: E6.7_p3

value: CTTTAA


title: inducible_ko_control_6_wk_No_5


title: inducible_ko_6_wk_No_4


title: inducible_ko_control_6_wk_No_1


title: inducible_ko_6_wk_No_6


title: E6.10_p3

value: GTTTAT


title: E6.6_p3

value: CTATAT


title: inducible_ko_6_wk_No_12


title: inducible_ko_control_6_wk_No_11


title: E6.4_p3

value: CAAATA


title: E6.9_p3

value: GTAATA


title: E6.5_p3

value: 16-cell stage

value: CATTAT


title: inducible_ko_2_wk_No_6

value: 14 days


title: E6.3_p3

value: ATTTCA


title: E6.2_p3

value: ATTCTA


title: inducible_ko_control_2_wk_No_4

value: Tamoxifen


title: E6.1_p3

value: ATTACT


title: inducible_ko_E16_No_1

value: embryonic day 16


title: E16.11_p1

value: ATATAG


title: E16.12_p1

value: ATCAAA


title: E16.13_p1

value: ATGAAT


title: inducible_ko_control_2_wk_No_1


title: inducible_ko_control_2_wk_No_2


title: inducible_ko_2_wk_No_16

value: HDAC1/2-loxP/loxP CX3CR1-CreERT2


title: 012B

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

department: Department of Medicine

institute: University of Wisconsin-Madison

description: expression.xlsx

data_processing:
Trimming-Sequencing reads were trimmed using the Skewer trimming program to remove sequencing adapters and bases with quality scores lower than Q20 (Jiang et al., 2014) Version 0.1.123: -q 20 -k 15 -l 25
Aligning-Trimmed reads were subsequently aligned to the Macaca mulatta reference genome (Zimin et al., 2014) using the STAR aligner(Dobin et al., 2013). Version 2.5.0a\n
Read count quantification-Quantification of expected read counts for each gene and isoform was calculated by RSEM (Li and Dewey, 2011). Version v1.2.31
Filtering-Transcripts were removed from the analysis if they had fewer than 5 reads in half of the samples.
Differential gene expression analysis-The remaining read counts were used for differential gene expression analysis using DESeq2 (Love et al., 2014), with the results used for pathway analysis via GSEA (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: Mmul_8.0.1 (rheMac8)
Supplementary_files_format_and_content: RNA_RawExpression_ReadCounts.xlsx; Single matrix file containing read counts for all transcripts and samples

organism: Macaca mulatta

source_name: Liver biopsy

extract_protocol:
Liver samples were homogenized in 1 mL TRIzol per 50 mg wet weight. Manual grinding with a pestle was used to pulverize the tissue, following which the sample was incubated for 5 min at room temperature. RNA extraction proceeded using a Direct-zol RNA kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. RNA was then submitted to the University of Wisconsin-Madison Biotechnology Center Sequencing Facility for high throughput RNA-Seq.
Each RNA library is generated following Illumina “TruSeq RNA Sample Preparation Guide and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA). Quality and quantity of finished libraries are assessed using an Agilent DNA1000 series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit HS Kit (Invitrogen, Carlsbad, California, USA), respectively. Each library is standardized to 2μM. Cluster generation is performed using a TruSeq Paired End Cluster Kit (v3) and the Illumina cBot, with libraries multiplexed for 2x100bp sequencing using the TruSeq 100bp SBS kit (v3) on an Illumina HiSeq2000. Images are analyzed using CASAVA 1.8.2.

tag: sample year

value: 2 year

tag: diet

value: CR


title: constituitive_ko_P0_No_76

value: HDAC1/2-loxP/loxP CX3CR1-Cre

value: no treatment

value: neonatal


title: E16.10_p1

value: 16-cell stage

value: ATACAA


title: E16.9_p1

value: ATAAAC


title: inducible_ko_control_6_wk_No_10

value: 45 days


title: 012A

description: expression.xlsx

value: 0 year


title: 011A

description: expression.xlsx


title: 011B

description: expression.xlsx


title: E16.7_p1

value: ACTTAT


title: constituitive_ko_control_P0_No_74


title: constituitive_ko_P0_No_73


title: E16.8_p1

value: AGATTA


title: inducible_ko_control_2_wk_No_3

value: Tamoxifen

value: 14 days


title: constituitive_ko_control_P0_No_71


title: 010A

description: expression.xlsx

value: Control


title: 010B

description: expression.xlsx


title: E16.5_p1

value: AATTCT


title: E16.4_p1

value: AATCTT


title: inducible_ko_2_wk_No_13

value: HDAC1/2-loxP/loxP CX3CR1-CreERT2


title: constituitive_ko_control_P0_No_69


title: E16.2_p1

value: AAGATT


title: 008B

description: expression.xlsx

value: 2 year

value: CR


title: E16.3_p1

value: AATACA


title: 009A

description: expression.xlsx


title: constituitive_ko_control_6_wk_No_400

value: no treatment


title: inducible_ko_2_wk_No_10


title: 007B

description: expression.xlsx


title: E10.16_p1

value: 16-cell stage

value: AAAACT


title: E10.15_p1

value: TCGGGC


title: E16.1_p1

value: AAAGTT