title: iCell_ChIP-Input-CREB_NT_KCl-0hr-15m_B1_1

description: iCell GABANeurons

data_processing:
For total RNA sequencing of human iCell cultures, strand-specific single-end reads nominally sequenced at 75 bp but occasionally shorter were 3'-truncated to 70bp and filtered to include only reads with unambiguous base calls (the ~0.1% of reads shorter than 70bp were discarded). Reads were then aligned to the hg19 or hg38 genome using BWA (v0.7.8) allowing up to 2 mismatches, zero gaps, and otherwise default parameters. The usual 24 chromosomal and MT alignment targets were supplemented with ~6.1 million short sequences comprising all possible intragenic subsets of ordered exons from the GRCh37.p5 RefSeq annotation, such that each sequence is of minimal length yet accommodates a 70-bp read spanning all junctions between consecutive exons with a subset; likewise, ~ 9.6 million such splice-junction sequences were included for the GRCh38.p2 RefSeq annotation. Typically 85-95% of all reads in each library were mappable and ~85-90% of these aligned uniquely; nonuniquely mapped reads were discarded.
Aligned total RNA-Seq reads were further analyzed using an in-house code MAPtoFeatures (M2F) that produces expression levels for individual genes and their exons. The following applies separately to the RefSeq annotations for human Build 37.3 assembly (7 Sept 2011) GRCh37.p5 and human assembly GRCh37.p2 (12 March 2015). The exons for all transcripts assigned to a gene based on RefSeq were merged (unioned); supplemented with the constructed library of splice-junction sequences, these defined each gene's complete mRNA target region. The total number of bases of all reads that overlapped a gene's exonic region were divided by region's total length to yield an average read Density (coverage). Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/70) (for 70-bp reads), where R = total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements. (RPKM units are proportional to normalized Density units: RPKM = Density/0.35). Relevant genic sense expression levels in M2F tables appear in column S_EXN_Density.
Differential-expression analyses were performed in R (v. 3.3.0) using edgeR to compare total RNA iCell samples that were stimulated with KCl to unstimulated samples. Stim time points at 15 minutes (6 samples), 1 hour (3), 2 hours (9), and 4 hours (3) were each compared to 9 samples at 0hr (unstim).  To produce a balanced normalization of Densities for each comparison, all RefSeq-annotated genes (23,202 in hg19; 24,681 in hg38) in all samples at each later time point were quantile normalized together with all samples at 0hr. These processed Densities were then converted back to read counts for edgeR input as follows:  divide each gene's Density by its sample's original normalization factor (10M/R)*(35/70), multiply by gene's number of exonic bases, divide by read length 70, and round up to nearest integer. These counts were input into edgeR, removing genes with zero expression and using all defaults and the BH correction for multiple comparisons, to obtain q-values to be measured against a desired false discovery rate (FDR).
Single-cell RNAseq reads were initially demultiplexed by Illumina BaseSpace to generate FASTQ files. Counts tables were created from the FASTQ files by an established pipeline: https://github.com/indrops/indrops. Counts tables were loaded into R (version 3.4.1) and analyzed using the Seurat package (Version 2.3.4 and 3.0.0). Cells were filtered by UMI, mitochondrial gene expression, and ribosomal gene expression. Data were log normalized and scaled and combined into one Seurat object. Cells were clustered and analyzed with PCA and UMAP. The final Seurat object contains 37,101 cells and 15 clusters.
For the single cell samples, we used iCellBio v.2 beads, so read 1 (R1) is the biological read and read 2 (R2) is the metadata read, containing the cell barcode and UMI. There are two cell barcode sequences and the combination of the two is the unique barcode for each cell. Structure of R2 is on the left of the top of the diagram (included as jpeg on series record).
Genome_build: GRCh37  (hg19; Feb, 2009)
Genome_build: GRCh38  (hg38; Dec, 2013)
Supplementary_files_format_and_content: MAPtoFeatures (M2F) tables have rows for genes and TAB-separated columns for various genic parameters, gene feature counts (for exons, introns, etc., individually and in total), and, for each feature and feature type, read counts, read-base counts, and normalized read Densities, all for reads that map sense or antisense to each gene. M2F LOG files document each run's read totals and summary statistics. Differential-expression tables from edgeR analyses have rows for genes and TAB-separated columns for: genic parameters, calculated fold-change (FC) ratios for KCl-stim at a time point, whether the mean change went up or down (UP.or.dn), inferred mean counts per million (CPM), reported p-value and BH-corrected q-value, various filtering results, numbers of samples with non0 expression and mean and SE log-RPKM values converted back to linear scale at each time, and read counts per sample input into edgeR. Single-cell counts tables list genes in rows, individual cells in TAB-separated columns; each entry is a UMI for a gene in a cell.

source_name: Input for CREB ChIPseq from iCell neurons, 0hr and 15m post-KCl stim, biorep 1

extract_protocol:
nuclear isolation from homogenized cultures
Nugen Ovation Ultralow Library System V1 using 2ng of starting DNA and performing 18 cycles of amplification

value: cultured human iPSC-derived neurons at ~DIV16

tag: time post-kcl stimulation

value: unstimulated

tag: biological replicate

tag: technical replicate

tag: chip epitope

value: none / input


title: iCell_ChIP-Input-CRTC1_NT_KCl-15m_B1_1

status: Public on Nov 27 2020

type: SRA

city: Boston

first: Gabriella

middle: Lutz

last: Boulting

state: MA

address: 200 Longwood Ave.

department: Neurobiology

country: USA

institute: Harvard Medical School

description: iCell GABANeurons

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Input for CRTC1 ChIPseq from iCell neurons, 15m post-KCl stim, biorep 1

growth_protocol: Manufacturer's protocol.

treatment_protocol: KCl membrane depolarization

tag: tissue

value: 15 minutes


title: iCell_ChIP-Input-Multi1_NT_KCl-0hr-15m

description:
iCell GABANeurons
Input for multiple ChIPseq experiments from iCell neurons, 0hr and 15m post-KCl stim, #1: CRTC1_NT_KCl-0hr_B3_1, CRTC1_NT_KCl-15m_B3_1, CREB_NT_KCl-0hr_B2_1, CREB_NT_KCl-15m_B2_1

value: multiple :CRTC1_NT_KCl-0hr_B3_1, CRTC1_NT_KCl-15m_B3_1, CREB_NT_KCl-0hr_B2_1, CREB_NT_KCl-15m_B2_1


title: iCell_ChIP-Input-CRTC1_NT_KCl-0hr-15m_B2_1

description: iCell GABANeurons

source_name: Input for CRTC1 ChIPseq from iCell neurons, 0hr and 15m post-KCl stim, biorep 2


title: iCell_ChIP-Input-Multi2_NT_KCl-0hr-15m

description:
iCell GABANeurons
Input for multiple ChIPseq experiments from iCell neurons, 0hr and 15m post-KCl stim, #2: H3K27ac_KCl-0hr-15min_B3_1,  H3K27ac_KCl-15min_B3_1, CRTC1_NT_KCl-0hr_B4_1,  CRTC1_NT_KCl-15m_B4_1, CREB_NT_KCl-0hr_B3_1, CREB_NT_KCl-15m_B3_1,  pCREB_NT_KCl-0hr_B2_1, pCREB_NT_KCl-15m_B2_1, CREB_NT_KCl-0hr_B4_1, CREB_NT_KCl-15m_B4_1.

value: multiple:H3K27ac_KCl-0hr-15min_B3_1,  H3K27ac_KCl-15min_B3_1, CRTC1_NT_KCl-0hr_B4_1,  CRTC1_NT_KCl-15m_B4_1, CREB_NT_KCl-0hr_B3_1, CREB_NT_KCl-15m_B3_1,  pCREB_NT_KCl-0hr_B2_1, pCREB_NT_KCl-15m_B2_1, CREB_NT_KCl-0hr_B4_1, CREB_NT_KCl-15m_B4_1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD010

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

value: brain

tag: source

value: AI

tag: target

value: ACA

tag: gender

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD001

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD007

value: female


title: iCell_ChIP-Input-H3K27ac2hr_B1-2_1

description: iCell GABANeurons

source_name: Input for H3K27ac ChIPseq from iCell neurons, 0hr and 2hrs post-KCl stim, bioreps 1 and 2

value: 1 and 2


title: iCell_ChIP-Input-H3K27ac15m_B1-2_1

description: iCell GABANeurons

source_name: Input for H3K27ac ChIPseq from iCell neurons, 0hr and 15m post-KCl stim, bioreps 1 and 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD006


title: T cells 1

city: Oklahoma City

first: Judith

middle: A.

last: James

state: Oklahoma

address: 825 NE 13th Street

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Libraries were evaluated for poor sample quality using FASTQC (version 0.11.8)
Adaptors and contaminating non-specific reads removed using BBTools (version38.56)
Reads were aligned to the GENCODE release 28 transcriptome using STAR (version 2.5.3a)
BAM files were then converted to a gene count matrix using StringTie (version 1.3.6)
Counts were normalized using the DESeq2 package (version 1.24.0) in R and transformed using variance stabilizing transformation for visualizations
All low expressed genes were removed prior to analysis, and outliers were identified and removed using hierarchical clustering
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel comma seperated values file with transcript counts

molecule: total RNA

source_name: PBMCs

extract_protocol:
PBMCs were sorted for CD66b-CD19-CD3+ T cells, CD66b-CD3-CD19+ B cells, CD66b-CD3-CD19-CD56-HLA-DR+CD14+CD16+/- monocytes using a FACS Aria III (BD Biosciences) and RNA was isolated using TRIZOL reagent (Invitrogen/Thermo Fischer (Waltham, MA), purified with Direct-zol RNA microprep kit (Zymo Research, Irvine, CA), and quantitated using 2100 Bioanalyzer (Agilent, Santa Clara, CA).
QuantSeq 3’ mRNA-sequencing library prep kit for Illumina (FWD) (Lexogen, Vienna, Austria) was used to create cDNA libraries, amplify and sequence 3 million reads/sample using NextSeq 550 (Illumina, San Diego, CA). 1 ug of total RNA was used for construction of the sequencing libraries and the manufacturer protocol was followed.

tag: manuscript subject id

tag: disease status

value: ANA-

tag: race

value: EA

tag: cell type

value: T cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD004


title: iCell_Single-cell_hg19_KCl-4hr_B3_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_4hr_B3.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 3, tech rep 3

extract_protocol:
single cell dissociation of culture using 5i method
according to 1CellBio hydrogel beads v2 manufacturer’s protocol

value: 4 hours


title: iCell_ChIP-Input-pCREB_NT_KCl-0hr-15m_B1_1

description: iCell GABANeurons

source_name: Input for pCREB ChIPseq from iCell neurons, 0hr and 15m post-KCl stim, biorep 1

value: cultured human iPSC-derived neurons at ~DIV16


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B11_AD004


title: iCell_Single-cell_hg19_KCl-4hr_B3_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B11_AD006


title: iCell_Single-cell_hg19_KCl-2hr_B3_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_2hr_B3.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 3, tech rep 3

value: 2 hours


title: iCell_Single-cell_hg19_KCl-4hr_B2_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_4hr_B2.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 2, tech rep 3


title: iCell_Single-cell_hg19_KCl-4hr_B2_2

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 2, tech rep 2


title: iCell_Single-cell_hg19_KCl-4hr_B3_2

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 3, tech rep 2


title: iCell_Single-cell_hg19_KCl-2hr_B3_2

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 3, tech rep 2


title: iCell_Single-cell_hg19_KCl-2hr_B2_2

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_2hr_B2.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 2, tech rep 2


title: iCell_ChIP-Input-CRTC1_NT_KCl-0hr_B1_1

description: iCell GABANeurons

source_name: Input for CRTC1 ChIPseq from iCell neurons, 0hr post-KCl stim, biorep 1

value: unstimulated

value: none / input


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B10_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B10_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B11_AD008


title: iCell_Single-cell_hg19_KCl-2hr_B2_3

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 2, tech rep 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B10_AD006


title: iCell_Single-cell_hg19_KCl-2hr_B2_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 2, tech rep 1


title: iCell_Single-cell_hg19_KCl-2hr_B1_2

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_2hr_B1.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 1, tech rep 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A9_AD012

source_name: C57BL/6J P56 Mouse Brain


title: iCell_Single-cell_hg19_KCl-2hr_B1_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A9_AD010


title: iCell_Single-cell_hg19_KCl-4hr_B2_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 4 hrs post-KCl stim, biorep 2, tech rep 1


title: iCell_Single-cell_hg19_KCl-2hr_B3_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 2 hrs post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A9_AD004


title: iCell_Single-cell_hg19_KCl-1hr_B3_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_1hr_B3.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 3, tech rep 3

value: 1 hours


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A8_AD010


title: iCell_Single-cell_hg19_KCl-1hr_B2_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_1hr_B2.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 2, tech rep 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B10_AD010


title: iCell_Single-cell_hg19_KCl-1hr_B3_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD012


title: iCell_Single-cell_hg19_KCl-1hr_B3_2

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 3, tech rep 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD004


title: iCell_Single-cell_hg19_KCl-1hr_B2_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 2, tech rep 1


title: iCell_Single-cell_hg19_KCl-1hr_B1_2

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_1hr_B1.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 1, tech rep 2


title: iCell_Single-cell_hg19_KCl-1hr_B1_1

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 1, tech rep 1


title: iCell_Single-cell_hg19_KCl-1hr_B2_2

source_name: Indrops single-cell RNA sequencing, iCell neurons, 1 hour post-KCl stim, biorep 2, tech rep 2


title: iCell_Single-cell_hg19_KCl-0hr_B3_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_0hr_B3.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 3, tech rep 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD006


title: iCell_Single-cell_hg19_KCl-0hr_B3_2

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 3, tech rep 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD002


title: iCell_Single-cell_hg19_KCl-0hr_B1_2

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_0hr_B1.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 1, tech rep 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A6_AD004


title: iCell_Single-cell_hg19_KCl-0hr_B2_3

description:
iCell GABANeurons
single cell
Boulting_2019_SuppData2_scRNAseq_Seurat.Rda
iCell_Single-cell_hg19_KCl_0hr_B2.counts.tsv.gz

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 2, tech rep 3


title: iCell_Single-cell_hg19_KCl-0hr_B2_2

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 2, tech rep 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A5_AD001

source_name: C57BL/6J P56 Mouse Brain


title: iCell_ChIP-pCREB_NT_KCl-15m_B1_1

description:
iCell GABANeurons
iCell_ChIP-pCREB_KCl-15m_B1-2_ext200bp_norm10M_Boulting.bw

source_name: S133 phophorylation of CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 1, tech rep 1

value: 15 minutes

value: pCREB


title: iCell_Single-cell_hg19_KCl-0hr_B1_1

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A4_AD010

value: brain

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A5_AD010

value: ACA

value: male


title: iCell_Single-cell_hg19_KCl-0hr_B3_1

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 3, tech rep 1


title: iCell_ChIP-pCREB_NT_KCl-0hr_B2_1

description:
iCell GABANeurons
iCell_ChIP-pCREB_KCl-0hr_B1-2_ext200bp_norm10M_Boulting.bw

source_name: S133 phophorylation of CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A4_AD008

value: female


title: iCell_ChIP-pCREB_NT_KCl-0hr_B1_1

source_name: S133 phophorylation of CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 1, tech rep 1


title: iCell_ChIP-H3K4me3_KCl-15m_B2_1

description:
iCell GABANeurons
iCell_ChIP-H3K4me3_KCl-15m_B1-2_ext200bp_norm10M_Boulting.bw

source_name: H3K4me3 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A4_AD006

value: Pons


title: iCell_ChIP-H3K27ac_KCl-2hr_B1_1

description:
iCell GABANeurons
iCell_ChIP-H3K27ac_KCl-2hr_B1-2_ext200bp_norm10M_Boulting.bw

source_name: H3K27ac ChIP-Seq, iCell neurons, 2 hours post-KCl stim, biorep 1, tech rep 1


title: iCell_ChIP-H3K4me3_KCl-15m_B1_1

source_name: H3K4me3 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A3_AD012


title: iCell_ChIP-H3K27ac_KCl-2hr_B2_1

source_name: H3K27ac ChIP-Seq, iCell neurons, 2 hours post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A3_AD008


title: iCell_Single-cell_hg19_KCl-0hr_B2_1

source_name: Indrops single-cell RNA sequencing, iCell neurons,unstimulated, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A4_AD001


title: iCell_ChIP-H3K27ac_KCl-0hr-2hr_B2_1

description:
iCell GABANeurons
iCell_ChIP-H3K27ac_KCl-0hr-2hr_B1-2_ext200bp_norm10M_Boulting.bw

source_name: H3K27ac ChIP-Seq, iCell neurons, unstimulated, for comparison with KCl-2hr, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A3_AD004


title: iCell_ChIP-H3K27ac_KCl-15m_B1_1

description:
iCell GABANeurons
iCell_ChIP-H3K27ac_KCl-15m_B1-2-3_ext200bp_norm10M_Boulting.bw

source_name: H3K27ac ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 1, tech rep 1


title: iCell_ChIP-pCREB_NT_KCl-15m_B2_1

source_name: S133 phophorylation of CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD006


title: iCell_ChIP-H3K27ac_KCl-0hr-2hr_B1_1

source_name: H3K27ac ChIP-Seq, iCell neurons, unstimulated, for comparison with KCl-2hr, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD002


title: iCell_ChIP-H3K27ac_KCl-0hr-15m_B3_1

source_name: H3K27ac ChIP-Seq, iCell neurons, unstimulated, for comparison with KCl-15min, biorep 3, tech rep 1


title: iCell_ChIP-CRTC1_NT_KCl-15m_B4_1

description:
iCell GABANeurons
iCell_ChIP-CRTC1_KCl-15m_B1-2-3-4_ext200bp_norm10M_Boulting.bw

source_name: CRTC1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 4, tech rep 1


title: iCell_ChIP-H3K27ac_KCl-15m_B2_1

source_name: H3K27ac ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 2, tech rep 1


title: iCell_ChIP-CRTC1_NT_KCl-15m_B2_1

source_name: CRTC1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A3_AD006

source_name: C57BL/6J P56 Mouse Brain


title: iCell_ChIP-H3K27ac_KCl-15m_B3_1

source_name: H3K27ac ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A3_AD001


title: iCell_ChIP-CRTC1_NT_KCl-15m_B1_1

source_name: CRTC1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 1, tech rep 1


title: iCell_ChIP-CRTC1_NT_KCl-15m_B3_1

source_name: CRTC1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A1_AD006


title: iCell_ChIP-CRTC1_NT_KCl-0hr_B3_1

description:
iCell GABANeurons
iCell_ChIP-CRTC1_KCl-0hr_B1-2-3-4_ext200bp_norm10M_Boulting.bw

source_name: CRTC1 ChIP-Seq, iCell neurons, unstimulated, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD010


title: iCell_ChIP-H3K27ac_KCl-0hr-15m_B1_1

source_name: H3K27ac ChIP-Seq, iCell neurons, unstimulated, for comparison with KCl-15min, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A1_AD004


title: iCell_ChIP-CRTC1_NT_KCl-0hr_B1_1

source_name: CRTC1 ChIP-Seq, iCell neurons, unstimulated, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD006


title: iCell_ChIP-CREB_NT_KCl-15m_B4_1

description:
iCell GABANeurons
iCell_ChIP-CREB_KCl-15m_B1-2-3-4_ext200bp_norm10M_Boulting.bw

source_name: CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 4, tech rep 1

value: CREB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A11_AD012


title: iCell_ChIP-CREB_NT_KCl-15m_B3_1

source_name: CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 3, tech rep 1


title: iCell_ChIP-CREB_NT_KCl-15m_B1_1

source_name: CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 1, tech rep 1


title: iCell_ChIP-CRTC1_NT_KCl-0hr_B4_1

source_name: CRTC1 ChIP-Seq, iCell neurons, unstimulated, biorep 4, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A11_AD006


title: iCell_ChIP-CREB_NT_KCl-0hr_B3_1

description:
iCell GABANeurons
iCell_ChIP-CREB_KCl-0hr_B1-2-3-4_ext200bp_norm10M_Boulting.bw

source_name: CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 3, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A11_AD007


title: iCell_ChIP-CREB_NT_KCl-0hr_B4_1

source_name: CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 4, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A11_AD004


title: f-CTX_ChIP-pCREB_B1_1

description:
BIDMC FB08
human_f-CTX_ChIP-pCREB_B1_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08, S133 phophorylation of CREB1 ChIP, biorep 1, nontruncated reads

extract_protocol:
nuclear isolation from postmortem tissue
Nugen Ovation Ultralow Library System V1 using 2ng of starting DNA and performing 18 cycles of amplification

value: human GW19 fetal frontal cortex tissue


title: iCell_ChIP-CREB_NT_KCl-0hr_B2_1

source_name: CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 2, tech rep 1


title: f-CTX_ChIP-Input_B2_1_trunc70bp

description:
BIDMC FB25
human_f-CTX_ChIP-INPUT_B2_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08,input library, biorep 2,  reads truncated to 70bp

value: human GW23 fetal frontal cortex tissue


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD010


title: iCell_ChIP-CREB_NT_KCl-15m_B2_1

source_name: CREB1 ChIP-Seq, iCell neurons, 15 minutes post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD006

source_name: C57BL/6J P56 Mouse Brain


title: f-CTX_ChIP-H3K27ac_B1_1

description:
BIDMC FB08
human_f-CTX_ChIP-H3K27ac_B1_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08, H3K27ac ChIP, biorep 1, nontruncated reads


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD004


title: f-CTX_ChIP-Input_B1_1

description:
BIDMC FB08
human_f-CTX_ChIP-INPUT_B1_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08,input library, biorep 1, nontruncated reads


title: f-CTX_ChIP-H3K27ac_B2_1_trunc70bp

description:
BIDMC FB25
human_f-CTX_ChIP-H3K27ac_B2_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB25, H3K27ac ChIP, biorep 2, reads truncated to 70bp


title: f-CTX_ChIP-pCREB_B2_1_trunc70bp

description:
BIDMC FB25
human_f-CTX_ChIP-pCREB_B2_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB25, S133 phophorylation of CREB1 ChIP, biorep 2, reads truncated to 70bp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H9_AD012

value: TH


title: f-CTX_ChIP-CREB_B2_1_trunc70bp

description:
BIDMC FB25
human_f-CTX_ChIP-CREB_B2_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB25, CREB1 ChIP, biorep 2, reads truncated to 70bp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H9_AD004

value: MOp

value: SSp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD001


title: iCell_ChIP-CREB_NT_KCl-0hr_B1_1

source_name: CREB1 ChIP-Seq, iCell neurons, unstimulated, biorep 1, tech rep 1

value: cultured human iPSC-derived neurons at ~DIV16

value: unstimulated


title: f-CTX_ChIP-CRTC1_B1_1_trunc70bp

description:
BIDMC FB08
human_f-CTX_ChIP-CRTC1_B1_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08, CRTC1 ChIP, biorep 1, reads truncated to 70bp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H8_AD008


title: iCell_ATAC_KCl-2hr_B2_1

description:
iCell GABANeurons
iCell_ATAC_KCl-2hr_B1-2-3_ext200bp_norm10M_Boulting.bw

source_name: iCell neurons, ATAC-Seq, 2hr post-KCl stim, biorep 2, tech rep 1

extract_protocol:
nuclear isolation from homogenized cultures
Nextera DNA Library Prep Kit (Illumina).

value: 2 hours


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_A10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H8_AD006


title: iCell_ATAC_KCl-2hr_B3_1

source_name: iCell neurons, ATAC-Seq, 2hr post-KCl stim, biorep 3, tech rep 1


title: iCell_ATAC_KCl-2hr_B1_1

source_name: iCell neurons, ATAC-Seq, 2hr post-KCl stim, biorep 1, tech rep 1


title: iCell_ATAC_KCl-15m_B3_1

description:
iCell GABANeurons
iCell_ATAC_KCl-15m_B1-2-3_ext200bp_norm10M_Boulting.bw

source_name: iCell neurons, ATAC-Seq, 15m post-KCl stim, biorep 3, tech rep 1

value: 15 minutes


title: iCell_ATAC_KCl-15m_B2_1

source_name: iCell neurons, ATAC-Seq, 15m post-KCl stim, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H7_AD004


title: iCell_ATAC_KCl-15m_B1_1

source_name: iCell neurons, ATAC-Seq, 15m post-KCl stim, biorep 1, tech rep 1


title: iCell_ATAC_KCl-0hr_B3_1

description:
iCell GABANeurons
iCell_ATAC_KCl-0hr_B1-2-3_ext200bp_norm10M_Boulting.bw

source_name: iCell neurons, ATAC-Seq, unstimulated, biorep 3, tech rep 1


title: f-CTX_ChIP-CRTC1_B2_1_trunc70bp

description:
BIDMC FB25
human_f-CTX_ChIP-CRTC1_B2_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB25, CRTC1 ChIP, biorep 2, reads truncated to 70bp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H7_AD002


title: iCell_ATAC_KCl-0hr_B2_1

source_name: iCell neurons, ATAC-Seq, unstimulated, biorep 2, tech rep 1


title: iCell_ChIP-H3K27ac_KCl-0hr-15m_B2_1

description:
iCell GABANeurons
iCell_ChIP-H3K4me3_KCl-15m_B1-2_ext200bp_norm10M_Boulting.bw

source_name: H3K27ac ChIP-Seq, iCell neurons, unstimulated, for comparison with KCl-15min, biorep 2, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H6_AD008

source_name: C57BL/6J P56 Mouse Brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H6_AD010


title: iCell_ATAC_KCl-0hr_B1_1

source_name: iCell neurons, ATAC-Seq, unstimulated, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H6_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H6_AD006


title: FTW-hiPSC#2.r1.RNA-seq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: Human FTW-induced pluripotent stem cell#2, repeat1, RNA-seq

data_processing:
We also examined global transcriptional profile of FTW-ESCs via RNA-sequencing (RNA-seq) and compared them with published mouse ESCs and EpiSCs datasets.
Principle component analysis (PCA) and unsupervised hierarchical clustering and correlation (UHC) analysis showed that FTW-ESCs clustered tightly as a group separated from both naïve ESCs and primed EpiSCs, indicating that FTW-ESCs acquired a distinct transcriptome profile (Fig. 1g and Extended Data Fig. 3a).
Analysis of pluripotency specific genes21 confirmed that FTW-ESCs exhibited a pluripotency profile different from ESCs and EpiSCs (Extended Data Fig. 3b).
Comparative analysis identified 79 genes uniquely expressed in FTW-PSCs using a 2-fold cut-off (p < 0.05) (Fig. 3h and Supplementary Table 1).
Gene ontology (GO) terms enriched in genes upregulated in FTW-ESCs were related to embryonic morphogenesis, cell fate commitment, formation of primary germ layers among others (Fig. 1i).
Genome_build: EquCab3.0
Genome_build: GRCh38.p12
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each sample.

molecule: polyA RNA

source_name: induced pluripotent stem cell

growth_protocol: C57BL/6 female mice (8–10 weeks old) were superovulated by intraperitoneal (IP) injection with 5 IU of PMSG (Prospec, Israel), followed by IP injection with 5 IU of hCG 48 h later. After mated with C57BL/6 male mice, embryos at 8-cell to morula stages were harvested at E2.75 (day of virginal plug = E0.5) in KSOM-Hepes (Wu et al., 2017) by flushing oviducts and uterine. They were cultured in the mKSOMaa (Wu et al., 2017) for overnight to form blastocysts until mESC injection in a humidified atmosphere containing 5% (v/v) CO2 and 5% (v/v) O2 at 37 °C. CD-1 females (8 weeks old or older) in natural estrous cycles were mated with CD-1 males. Blastocysts were harvested at E3.5 by flushing uterine horns, and cultured until Eq-iPSC injection.Vitrified equine embryos were thawed in a series of pre-warmed solutions: 0.25, 0.15, and 0 M sucrose in Hanks buffer (Gibco) containing 20% FBS. After thawing, embryos were cultured on the MEF in FTW medium overnight until blastocysts formed in a humidified atmosphere containing 5% (v/v) CO2 and 20% (v/v) O2 at 37 °C.

extract_protocol:
RNA  extraction was performed using a RNeasy Mini Kit (QIAGEN) using DNase treatment (QIAGEN).
RNA was analyzed using a 2100 Bioanalyzer (Aglient Technologies, USA). (Transcripts per Kilobase Million)

value: FTW-induced pluripotent stem cell


title: FTW-hiPSC#1.r2.RNA-seq

description: Human FTW-induced pluripotent stem cell#1, repeat2, RNA-seq


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD012

value: brain


title: FTW-hiPSC#2.r2.RNA-seq

description: Human FTW-induced pluripotent stem cell#2, repeat2, RNA-seq


title: f-CTX_ChIP-CREB_B1_1

description:
BIDMC FB08
human_f-CTX_ChIP-CREB_B1_ext200bp_norm10M_Boulting.bw

source_name: human fetal frontal cortex FB08, CREB1 ChIP, biorep 1, nontruncated reads


title: FTW-hiPSC#1.r1.RNA-seq

description: Human FTW-induced pluripotent stem cell#1, repeat1, RNA-seq


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD004


title: Lung CD45iv- CD4+CD44+ T cells

city: Rochester

first: Yougnmin

last: Son

address: 200 1st Stabile 8-21

institute: Mayo Clinic

data_processing:
Paired-end sequencing was performed using an Illumina HiSeq 2500 in rapid-run mode.
CellRanger software package (10x Genomics) were used to align and quantify sequencing data from 10x Genomics.
All scRNA-seq analyses were performed in R  using the package Seurat (version 2.0)
Genome_build: mm10
Supplementary_files_format_and_content: raw_gene_bc_matrices

source_name: Lung CD4+ T cells

extract_protocol:
Sorted CD45i.v.-CD4+CD44Hi T cells from pooled lung cells of mice (5 mice) infected with influenza virus (28 d.p.i.) were loaded on the Chromium Controller (10x Genomics).
Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent kit (10x Genomics)

tag: infection

value: Influenza A/PR8/34 (28 d.p.i.)

value: Lung

tag: cell markers


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H4_AD006


title: mPFC, MG Depletion/Dep #39

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: MG Depletion/Dep #39 mPFC abundance

data_processing:
Adapters were trimmed and filtered using tagseq_clipper.pl and tagseq_trim_launch.pl https://github.com/z0on/tag-based_RNAseq
Raw 3'UTR biased-sequencing files were evaluated for quality control using FastQC (0.11.8).
Reads were mapped to the mouse reference genome (UCSC, mm10) using the alignment tool Bowtie2 (v2.3.4.3).
HTSeq (v.0.11.0), was used for counting mapped sequencing reads.
Quantified read counts were normalized and analyzed for differential expression using DESeq2 (v 1.10.1), between microglia intact and microglia depleted animals, within the R statistical computing environment (v3.5.1)
Genome_build: GRCm38.p6.genome.fa.gz from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: medial prefrontal cortex

extract_protocol:
medial prefrontal cortex was fresh dissected, flash frozen on dry ice.The remainder of the brain was flash frozen in OCT and sliced at 300um. The CeA was then punched and the RNA from each region was isolated using Trizol reagent and MagMAX-96 Total RNA Isolation Kit . DNA contamination removed using DNA-free kit.  (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA was fragmented then first strand synthesis occurred using majority deoxycytidine nucleotides which served as an anchor for the switch oligos. swOligo used: /5Me-isodC/iisodG/iMeisodC/CCATGCGGCTACACGACGC TCTTCCGATCTNNMWrGrGrG. cDNA strand with portions of adapter were added then amplified, followed by second PCR to add index portion of the adapter.
Samples were then pooled, size selected with Pippin then sequenced on a Single End Run using the HiSeq 2500 for mPFC and NovaSeq 6000 for CeA for a read depth of ~4 million reads per sample

treatment_protocol: Treated with PLX5622 (1200mg/kg) for 28 days prior to beginning chronic intermittent ethanol exposure paired with two-bottle choice drinking (15%) for four weeks, sacrified 24 hours after last ethanol exposure.

value: medial prefrontal cortex

value: post-natal day 119

tag: chow

tag: ethanol exposure

value: Dependent (Dep)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H5_AD002

value: female


title: mPFC, MG Depletion/Dep #38

description: MG Depletion/Dep #38 mPFC abundance


title: mPFC, MG Depletion/Dep #37

description: MG Depletion/Dep #37 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD010

value: ACA

value: male


title: Embryonic stem cells-Control, rep 3

type: RNA

city: Tianjin

first: Yuhong

last: Bian

address: 10 Poyanghu Road, West Area,  Tuanbo New Town, Jinghai District

institute: Tianjin University of Traditional Chinese Medicine

hyb_protocol: A total of 10 μg of cRNA from each sample was hybridized with the mouse MG 430 2.0 GeneChips Affymetrix for 16 h at 45˚C. Following hybridization, the microarray was washed and stained in an automated fluidics station (Affymetrix GeneChip Hybridization Wash and Stain kit).

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

data_processing: Microarray data were assessed using the DNA-Chip Analyser (dChip version 2010) with a model-based computation. All arrays were normalized to a common baseline array, and the expression levels of each gene in all samples were computed using the PM‐MM (Perfect Match‐Mis Match) differences for all probes in a probe set.

label: biotin

source_name: Mouse embryonic inner cell masses

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual,  Affymetrix).

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

value: Blastula

tag: genotype

value: Blastocyst at day 3.5

value: Mouse embryonic stem cells D3


title: Embryonic stem cells-treated Aristolochic acid-48h, rep 2


title: Embryonic stem cells-Control, rep 2


title: Embryonic stem cells-Control, rep 1


title: mPFC, MG Depletion/Dep #30

description: MG Depletion/Dep #30 mPFC abundance


title: Embryonic stem cells-treated Aristolochic acid-48h, rep 3


title: mPFC, MG Depletion/Dep #40

description: MG Depletion/Dep #40 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD008

value: TH


title: Embryonic stem cells-treated Aristolochic acid-48h, rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD002

value: MOp

value: SSp


title: mPFC, MG Depletion/Dep #08

description: MG Depletion/Dep #08 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD006


title: mPFC, MG Depletion/Dep #07

description: MG Depletion/Dep #07 mPFC abundance


title: mPFC, MG Depletion/Dep #29

description: MG Depletion/Dep #29 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H1_AD010


title: mPFC, MG Depletion/Dep #06

description: MG Depletion/Dep #06 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H1_AD002


title: mPFC, Control Diet/Dep #28

description: Control Diet/Dep #28 mPFC abundance

value: Control Diet


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H11_AD002


title: mPFC, Control Diet/Dep #11

description: Control Diet/Dep #11 mPFC abundance


title: mPFC, Control Diet/Dep #26

description: Control Diet/Dep #26 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H10_AD006


title: FTW-eqESC.r2.H3K27me3

description: Equine FTW-embryonic stem cell, repeat2, H3K27me3 (ChIP-seq)

data_processing:
We examined the global deposition of histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 27 trimethylation (H3K27me3) in FTW-ESCs using ChIP-sequencing (ChIP-seq) 22.
Our analysis revealed that H3K4me3 levels were similar between FTW-ESCs and naïve ESCs, which were higher than primed EpiSCs.
Interestingly, a pronounced reduction of H3K27me3 deposition was observed in FTW-ESCs (Fig 1j).
These results indicate that FTW-ESCs are distinct from mouse ESCs and EpiSCs at both transcriptome and epigenome levels, and presumably exist in an intermediate pluripotent state between naïve and primed.
Genome_build: EquCab3.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bigWig file for each sample.

organism: Equus ferus

source_name: Embryonic cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with an antibody.
ChIP-Seq libraries were prepared from size-selected ChIP DNA according to the standard Illimina library preparation protocol

value: FTW-embryonic stem cell

tag: antibody


title: mPFC, Control Diet/Dep #10

description: Control Diet/Dep #10 mPFC abundance


title: MKN7_mock_infection

city: Itabashi-Ku

first: Yu

last: Takahashi

state: Tokyo

department: gastroenterology

country: Japan

institute: Nihon University

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45 deg C, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

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

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip Operating Software v1.4. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: gastric cancer cell line

label_protocol: In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.

growth_protocol: The cell lines were incubated in a 37C incubator using D-MEM + 10% fetal bovine serum.

extract_protocol: Total RNA was extracted from cells using the Isogen reagent (Nippon Gene, Toyama, Japan), converted to cDNA by using the Prime Script reverse transcriptase (Takara, Shiga, Japan) as per the manufacturer’s instructions.The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned by Sample Cleanup Module (Affymetrix).

treatment_protocol: Retrovirus infection was used to introduce pMXs-Cdx1-IRESPuro or pMXs-Cdx2-IRESPuro or pMXs-IRESPuro vector into cell lines. Those cell lines were selected 1.0 ug/ml Puromycin containing buffer 72hours after the infection. The cells were incubated for seven days after the infection and until then the cells were completed of selection.

tag: cell line

tag: transduction

value: IP


title: mPFC, Control Diet/Dep #27

description: Control Diet/Dep #27 mPFC abundance

tag: strain

tag: tissue


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H12_AD006

tag: age

value: brain

tag: source


title: TMK1_mock_infection


title: TMK1_Cdx2_overexpressed


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H11_AD001

tag: target

tag: gender


title: TMK1_Cdx1_overexpressed


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H12_AD004


title: MKN7_Cdx2_overexpressed


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H10_AD002


title: mPFC, Control Diet/Dep #03

description: Control Diet/Dep #03 mPFC abundance


title: TMK1

value: control


title: mPFC, Control Diet/Dep #09

description: Control Diet/Dep #09 mPFC abundance

value: medial prefrontal cortex


title: BC2

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
Cellranger count pipeline
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Fresh Her2+ breast tumour biopsy

extract_protocol: As per manufacturer's (10X genomics) protocol

value: Fresh Her2+ breast tumour biopsy

tag: gating strategy

tag: dissociation protocol

value: Ficol gradient followed by cryopreservation in 10% DMSO


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD010


title: FTW-eqiPSC.r2.H3K4me3

description: Equine FTW-induced pluripotent stem cell, repeat2, H3K4me3 (ChIP-seq)

tag: cell type

value: FTW-induced pluripotent stem cell


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H10_AD004

value: female


title: BC1

source_name: Fresh triple-negative (TNBC) breast tumour biopsy


title: MS023_4

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

description:
countsMatrix.tsv
countsMatrix_normalized.csv
de_stats.csv

data_processing:
Illumina bcl2fastq2.17 was used for basecalling.
Sequenced reads were trimmed from adaptor sequence, polyA/T sequences and low quality bases (quality score <10) at the beginning and end of all reads using cutadapt1.10. Reads shorter than 30bp were discarded.
Trimmed reads were mapped to the H. sapiens reference genome GRCh38 using STAR36 using Ensembl annotations (v.92) with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04
Gene counts were generated with htseq-count v.0.6.1p1, in intersection-strict mode. Counts normalization and differential expression analysis were done using Deseq2 v.1.10.1.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample.
Supplementary_files_format_and_content: A comma separated file that contains the differential expression results between treatments and control (DMSO) for all genes.

source_name: HT-29 cells

growth_protocol: HT-29 cells were plated in 6-well plates (30,000 cells/well) in 1.5ml of regular growth medium

extract_protocol:
RNA was eluted using RNeasy Mini Kit (Qiagen, #74104) according to the manufacture protocol.
PolyA fraction (mRNA) was purified from 500ng of total RNA following by fragmentation and the generation of double-stranded cDNA. Then, end repair, A base addition, adapter ligation and PCR amplification steps were performed

treatment_protocol: 2 Hours after plating, cells were treated with DMSO, entinostat (1.5µM) or MS023 (5µM). RNA was extracted after 5 days.

tag: treatment


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_H10_AD008

value: ACA


title: mPFC, Control Diet/Dep #04

description: Control Diet/Dep #04 mPFC abundance

value: post-natal day 119

value: Dependent (Dep)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD006


title: mPFC, Control Diet/Dep #01

description: Control Diet/Dep #01 mPFC abundance


title: mPFC, MG Depletion/Non-Dep #47

description: MG Depletion/Non-Dep #47 mPFC abundance

value: Non-Dependent (Non-Dep)


title: FTW-eqiPSC.r2.H3K27me3

description: Equine FTW-induced pluripotent stem cell, repeat2, H3K27me3 (ChIP-seq)


title: FTW-eqiPSC.r2.Input

description: Equine FTW-induced pluripotent stem cell, repeat2, Input DNA (ChIP-seq)

value: Input DNA


title: FTW-eqiPSC.r1.H3K4me3

description: Equine FTW-induced pluripotent stem cell, repeat1, H3K4me3 (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD004

value: MOp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD008

value: TH


title: MS023_3


title: mPFC, MG Depletion/Non-Dep #45

description: MG Depletion/Non-Dep #45 mPFC abundance


title: NT4

value: DMSO


title: mPFC, MG Depletion/Non-Dep #46

description: MG Depletion/Non-Dep #46 mPFC abundance


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD002

value: SSp


title: MKN7_Cdx1_overexpressed


title: MKN7


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G9_AD001


title: mPFC, MG Depletion/Non-Dep #23

description: MG Depletion/Non-Dep #23 mPFC abundance


title: FTW-eqiPSC.r1.Input

description: Equine FTW-induced pluripotent stem cell, repeat1, Input DNA (ChIP-seq)


title: MS023_2


title: MS023_1


title: FTW-eqESC.r2.H3K4me3

description: Equine FTW-embryonic stem cell, repeat2, H3K4me3 (ChIP-seq)

value: FTW-embryonic stem cell


title: mPFC, MG Depletion/Non-Dep #24

description: MG Depletion/Non-Dep #24 mPFC abundance


title: FTW-eqiPSC.r1.H3K27me3

description: Equine FTW-induced pluripotent stem cell, repeat1, H3K27me3 (ChIP-seq)


title: FTW-eqESC.r2.Input

description: Equine FTW-embryonic stem cell, repeat2, Input DNA (ChIP-seq)


title: mPFC, MG Depletion/Non-Dep #22

description: MG Depletion/Non-Dep #22 mPFC abundance


title: NT2


title: FTW-eqESC.r1.H3K27me3

description: Equine FTW-embryonic stem cell, repeat1, H3K27me3 (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD010

value: brain

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD006


title: NT3


title: Ent2

value: Entinostat


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD004


title: mPFC, MG Depletion/Non-Dep #21

description: MG Depletion/Non-Dep #21 mPFC abundance

value: medial prefrontal cortex


title: NT1


title: FTW-eqESC.r1.H3K4me3

description: Equine FTW-embryonic stem cell, repeat1, H3K4me3 (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD008


title: FTW-eqESC.r1.Input

description: Equine FTW-embryonic stem cell, repeat1, Input DNA (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD002


title: iCell_ChIP-CRTC1_NT_KCl-0hr_B2_1

description:
iCell GABANeurons
iCell_ChIP-CRTC1_KCl-0hr_B1-2-3-4_ext200bp_norm10M_Boulting.bw

source_name: CRTC1 ChIP-Seq, iCell neurons, unstimulated, biorep 2, tech rep 1

value: cultured human iPSC-derived neurons at ~DIV16

tag: time post-kcl stimulation

value: unstimulated

tag: biological replicate

tag: technical replicate

tag: chip epitope


title: mPFC, MG Depletion/Non-Dep #13

description: MG Depletion/Non-Dep #13 mPFC abundance

tag: chow

tag: ethanol exposure


title: mPFC, Control Diet/Non-Dep #35

description: Control Diet/Non-Dep #35 mPFC abundance

value: Control Diet


title: mPFC, Control Diet/Non-Dep #36

description: Control Diet/Non-Dep #36 mPFC abundance


title: FTW-eqESC#2.r2.RNA-seq

description: Equine FTW-embryonic stem cell#2, repeat2, RNA-seq

data_processing:
We also examined global transcriptional profile of FTW-ESCs via RNA-sequencing (RNA-seq) and compared them with published mouse ESCs and EpiSCs datasets.
Principle component analysis (PCA) and unsupervised hierarchical clustering and correlation (UHC) analysis showed that FTW-ESCs clustered tightly as a group separated from both naïve ESCs and primed EpiSCs, indicating that FTW-ESCs acquired a distinct transcriptome profile (Fig. 1g and Extended Data Fig. 3a).
Analysis of pluripotency specific genes21 confirmed that FTW-ESCs exhibited a pluripotency profile different from ESCs and EpiSCs (Extended Data Fig. 3b).
Comparative analysis identified 79 genes uniquely expressed in FTW-PSCs using a 2-fold cut-off (p < 0.05) (Fig. 3h and Supplementary Table 1).
Gene ontology (GO) terms enriched in genes upregulated in FTW-ESCs were related to embryonic morphogenesis, cell fate commitment, formation of primary germ layers among others (Fig. 1i).
Genome_build: EquCab3.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each sample.


title: Ent1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G7_AD008

value: ACA

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G8_AD001


title: mPFC, MG Depletion/Non-Dep #16

description: MG Depletion/Non-Dep #16 mPFC abundance

value: post-natal day 119


title: FTW-eqESC#1.r1.RNA-seq

description: Equine FTW-embryonic stem cell#1, repeat1, RNA-seq


title: Ent4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G7_AD002


title: mPFC, Control Diet/Non-Dep #34

description: Control Diet/Non-Dep #34 mPFC abundance

value: Non-Dependent (Non-Dep)


title: FTW-eqiPSC#2.r2.RNA-seq

description: Equine FTW-induced pluripotent stem cell#2, repeat2, RNA-seq

value: FTW-induced pluripotent stem cell


title: mPFC, Control Diet/Non-Dep #33

description: Control Diet/Non-Dep #33 mPFC abundance


title: SC-His-Ade-Arg+ATc Rep 5

city: New York

first: Amir

last: Momen-Roknabadi

state: NY

address: 1150 St. Nicholas Ave Room 406

institute: Colombia University

description: Plasmid DNA

data_processing:
The read 2 does not have any useful information and is discarded. We did paired-end sequencing for compatibility with an ongoing project in the lab
Clip 3' universal adapter sequence of read 1 with cutadapt
Clip  5' custom index sequence and demultiplex with cutadapt
Reads aligned with bowtie2  version 2.2.6 to the gRNA library
Final matrix of Counts generated with a custom script in python 2.7.15 and R
Supplementary_files_format_and_content: CSV

organism: Saccharomyces cerevisiae

source_name: Bacterial Library Rep 2

growth_protocol: The transformed bacteria were grown in 1L of semisolid LB plus 100 μg/ ml ampicillin (0.35% Seaprep Agarose, Lonza) overnight at 37C.  The yeast transformed library was grown in semisolid SC-His+glu media (0.35% Seaprep Agarose) for 48 hours at 30C. For this study, we inoculated 250ml of the following three semisolid media with a number of cells equivalent to 1 OD660 unit of the library: A) SC-His with ATc, B) SC-His-Arg-Ade with ATc C) SC-His-Arg-Ade without ATc.

extract_protocol:
To extract the plasmids, 50 OD660 of cells were pooled and resuspended in 2 ml SE buffer (0.9M sorbitol, 0.1M EDTA pH 8.0), 200 µl Zymolyase 100T (2 mg/ml) and 2 µl b-mercaptoethanol and incubated at 37°C for one hour, followed by standard mini prep extraction per manufacturer’s instructions (Promega).
The library spacers were amplified and extended as described by Smith et al. 2016. To generate the library, amPL43 was maxiprepped (Qiagen, Hilden, Germany) and cut with NotI. Gibson Assembly was used to clone the oligos in the NotI site of amPL43. The library was transformed into DH5a E. coli (NEB C2987H).
Other: DNA amplicon sequencing

treatment_protocol: The library can be induced in the presence of 250 ng/mL ATc

tag: media

value: Semisolid media

tag: atc

value: Yes

value: Yeast


title: SC-His-Ade-Arg+ATc Rep 2

description: Plasmid DNA

source_name: Bacterial Library Rep 1


title: SC-His-Ade-Arg+ATc Rep 4

description: Plasmid DNA


title: Ent3


title: mPFC, Control Diet/Non-Dep #19

description: Control Diet/Non-Dep #19 mPFC abundance

tag: strain

tag: tissue


title: FTW-eqiPSC#2.r1.RNA-seq

description: Equine FTW-induced pluripotent stem cell#2, repeat1, RNA-seq


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G7_AD001

tag: age

tag: source

value: MOp

value: SSp


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G6_AD001

value: brain

tag: target

tag: gender


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G6_AD010

value: TH

value: male


title: FTW-eqiPSC#1.r2.RNA-seq

description: Equine FTW-induced pluripotent stem cell#1, repeat2, RNA-seq


title: RIP_w1118_IgG_REP5

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

data_processing:
Illumina bcl2fastq v2.20 software was used for basecalling and demultiplexing.
Reads were preprocessed (quality <Q30, adapters stripped) with TrimGalore, then aligned to the Drosophila melanogaster genome r6.28 with STAR. Aligned reads were deduplicated using UMIs, and gene read counts were normalized by library size.
Genome_build: dmel6
Supplementary_files_format_and_content: rawcounts_genes.tsv: Tab-delimited text file includes raw read counts for each sample.

organism: Drosophila melanogaster

source_name: whole brain

growth_protocol: Drosophila melanogaster stocks used were the w1118 and the mutant Ythdf#0/#0.

extract_protocol:
Upon treatment the supernatant was separated from the beads and RNA was extracted using Trizol reagent.
Strand-specific, rRNA depleted libraries were generated with the Ovation® SoLo RNA-Seq System plus Drosophila AnyDeplete Probe Mix (Tecan Genomics).

treatment_protocol: For RIP from pupal heads for endogenous Fmr1: 200 heads per each genotype were collected in PBS on ice and subsequently re-suspended in 100 µl of Lysis Buffer (10 mM Tris-HCl pH 7.4, 140 mM NaCl, 0.5%Triton X-100, 1 mM DTT, 2 mM EDTA) supplemented with protease, phosphatase and RNase inhibitors. The heads were lysed with a motor pestle and left on ice for 20’. The cell debris was removed by centrifugation at 12000 g for 10 minutes at 4°C, 1/10 of the volume was taken as an input and kept at -80 while the rest of the supernatant was divided in two and combined with either 20 µl of anti–Fmr1 5B6 and 20 µl of anti–Fmr1 5A11 or to 1.5 µl of mouse IgG together with 50 µl of Protein G Dynabeads in lysis buffer. The lysate was incubated with the beads- antibody rotating head-over-end at 4°C over-night. The day after the beads were washed three times for 10 minutes and subsequently resuspended in 100 µl of lysis buffer that were further treated with 40 µg of Proteinase K for 30’ at 55°C.

tag: stock

tag: genotype

value: wild type

value: whole brain

tag: ip

value: IgG


title: RIP_w1118_IgG_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: Eq-EEF.r2.RNA-seq

description: Equine embryonic fibroblast, repeat2, RNA-seq

tag: cell type

value: embryonic fibroblast


title: SC-His-Ade-Arg+ATc Rep 1

description: Plasmid DNA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G5_AD001


title: mPFC, Control Diet/Non-Dep #17

description: Control Diet/Non-Dep #17 mPFC abundance

value: medial prefrontal cortex

value: Control Diet


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G5_AD012

value: ACA

value: female


title: FTW-eqESC#2.r1.RNA-seq

description: Equine FTW-embryonic stem cell#2, repeat1, RNA-seq

value: FTW-embryonic stem cell


title: SC-His+ATc Rep 3

description: Plasmid DNA

value: Semisolid media


title: RIP_w1118_IgG_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: mPFC, Control Diet/Non-Dep #20

description: Control Diet/Non-Dep #20 mPFC abundance

value: post-natal day 119

value: Non-Dependent (Non-Dep)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G4_AD006

value: MOp


title: RIP_w1118_IgG_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: SC-His+ATc Rep 5

description: Plasmid DNA

value: Yes

value: Yeast


title: FTW-eqESC#1.r2.RNA-seq

description: Equine FTW-embryonic stem cell#1, repeat2, RNA-seq


title: SC-His-Ade-Arg+ATc Rep 3

description: Plasmid DNA


title: SC-His+ATc Rep 4

description: Plasmid DNA


title: LPS Female; family 2868 [2868LPS-R1F]

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

description:
LPS Female; family 2868
2868LPS-R1F

data_processing:
Align paired end sequencing reads to reference genome MM10 using program STAR_2.4.0
Convert SAM files from START to binary BAM files, and sort the BAM files
Map reads to location of known mouse genes
Count number of reads uniquely mapped to each gene
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: A tab-delimited txt file with read count for each sample, of all known mouse genes

source_name: placenta

growth_protocol: Mouse fetus

extract_protocol:
Total RNA was extracted from frozen placenta using TRIzol® Reagent (Invitrogen), followed by Qiagen RNeasy® Mini Columns following manufacturer’s instructions.
Multiplexed libraries were created using the Illumina TruSeq Stranded Tatal RAN Sample Prep kit with Ribo-Zero following manufacturer’s instructions

treatment_protocol: A mini-laparotomy was performed on CD-1 timed pregnant mice at gestational day 17. Mice then received intrauterine injections of liposaccharide (LPS) from Escherichia coli ( 50ug/100μl phosphate buffered saline/animal) or PBS (100μl/animal). Dams were allowed to recover for 6 hours prior to placental tissue collection.

value: placenta

tag: treatment

value: LPS

value: Female

tag: family


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G4_AD004

source_name: C57BL/6J P56 Mouse Brain

value: brain

value: SSp


title: RIP_w1118_Fmr1_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: wild type

value: whole brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G4_AD001


title: SC-His+ATc Rep 2

description: Plasmid DNA


title: Eq-EEF.r1.RNA-seq

description: Equine embryonic fibroblast, repeat1, RNA-seq

value: embryonic fibroblast


title: FTW-eqiPSC#1.r1.RNA-seq

description: Equine FTW-induced pluripotent stem cell#1, repeat1, RNA-seq

value: FTW-induced pluripotent stem cell


title: LPS Female; family 2870 [2870LPS-L2F]

description:
LPS Female; family 2870
2870LPS-L2F


title: LPS Female; family 2867 [2867LPS-R1F]

description:
LPS Female; family 2867
2867LPS-R1F


title: RIP_w1118_Fmr1_REP5

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: SC-His-ATc Rep 2

description: Plasmid DNA

value: No


title: RIP_w1118_IgG_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: IgG


title: LPS Male; family 2870 [2870LPS-R1M]

description:
LPS Male; family 2870
2870LPS-R1M

value: Male


title: SC-His-ATc Rep 3

description: Plasmid DNA

value: Semisolid media


title: LPS Female; family 2870 [2870LPS-L1F]

description:
LPS Female; family 2870
2870LPS-L1F


title: SC-His+ATc Rep 1

description: Plasmid DNA


title: RIP_w1118_Fmr1_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: RIP_w1118_Fmr1_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G3_AD008

value: ACA

value: TH

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G3_AD012


title: RIP_w1118_Fmr1_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: LPS Male; family 2867 [2867LPS-L2M]

description:
LPS Male; family 2867
2867LPS-L2M


title: Yeast Rep 4

description: Plasmid DNA

value: Yeast


title: SC-His-ATc Rep 1

description: Plasmid DNA


title: LPS Male; family 2868 [2868LPS-L2M]

description:
LPS Male; family 2868
2868LPS-L2M

value: placenta


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G3_AD006

value: MOp


title: RIP_CG6422_IgG_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: LPS Male; family 2867 [2867LPS-L1M]

description:
LPS Male; family 2867
2867LPS-L1M

value: LPS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G3_AD002

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G4_AD002

value: SSp


title: Yeast Rep 3

description: Plasmid DNA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G2_AD004


title: RIP_CG6422_IgG_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G1_AD010

value: male


title: RIP_CG6422_Fmr1_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: whole brain


title: Control Female; family 2863 [2863C-L2F]

description:
Control Female; family 2863
2863C-L2F

value: Control

value: Female


title: Control Female; family 2865 [2865C-L1F]

description:
Control Female; family 2865
2865C-L1F


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G1_AD008


title: Yeast Rep 5

description: Plasmid DNA

value: No


title: Control Female; family 2864 [2864C-L3F]

description:
Control Female; family 2864
2864C-L3F


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G1_AD006


title: Control Female; family 2863 [2863C-L1F]

description:
Control Female; family 2863
2863C-L1F


title: Yeast Rep 2

description: Plasmid DNA


title: Control Male; family 2866 [2866C-L1M]

description:
Control Male; family 2866
2866C-L1M


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G12_AD012


title: RIP_CG6422_Fmr1_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G12_AD004


title: RIP_CG6422_IgG_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: IgG


title: Yeast Rep 1

description: Plasmid DNA


title: HSC TKO rep3

city: Bronx

first: Kristina

last: Ames

address: 1300 Morris Park Avenue, Chanin 410

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Illumina's Real Time Analysis (RTA) software was used for the base calling,
bcl2Fastq software was used to convert BCL to fastq file
Flanking adapter sequences were removed with trim galore (v.0.3.7), Sequence quality was assessed using fastqc (v.0.11.4)
Adapter-trimmed fastq files were aligned to the mouse mm10 genome, and read counts per gene were determined, using the splice-aware aligner STAR (v2.5.1b)
Differential gene expression was assessed with R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: text files

source_name: Bone

growth_protocol: Whole bone marrow cells (TKO, δ KO, WT)  were transplanted into the lethally irradiated recipients. Animals we maintained at regular mouse facility.

extract_protocol:
BM cells were harvested from femurs, tibiae, pelvises and vertebrae by gentle crushing in RPMI medium. Low-density BM mononuclear cells (BMMNCs) were isolated by density gradient centrifugation using Ficoll Histopaque 1083, cells were pooled from all 7 recipients/ group, and stained with an anti-mouse antibody coctail. Donor-derived HSCs (Lin-cKit+Sca1+Flk2-CD48-CD150+) were sorted using MoFlo Astrios Cell Sorter. HSC cells were directly sorted into 50μl RNA extraction buffer and total RNA was extracted according to the manufacturer’s protocol  (ARCTURUS PicoPure RNA Isolation Kit). Samples were shipped to BGI.
cDNA was amplified from total RNA using the Ovation® RNA‑Seq System V2 at BGI.

treatment_protocol: Transplanted whole bone marrow (TKO, δ KO, WT) recipients were injected with pIpC 250μg x2 48 hours apart to excise floxed alleles.  Bone marrow cells were harvested at 4 weeks post PIPC.

value: Bone

value: Hematopoietic stem cells

value: donor derived sorted hematopoietic stem cells


title: HSC WT rep1

value: WT, Mx1-Cre


title: HSC WT rep3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G12_AD001

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: female


title: HSC WT rep2


title: RIP_CG6422_IgG_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: Control Male; family 2864 [2864C-L2M]

description:
Control Male; family 2864
2864C-L2M

value: Male


title: Control Male; family 2865 [2865C-L2M]

description:
Control Male; family 2865
2865C-L2M

value: placenta


title: RIP_CG6422_Fmr1_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: HSC TKO rep2


title: INPUT_w1118_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: wild type


title: Control Male; family 2864 [2864C-L1M]

description:
Control Male; family 2864
2864C-L1M


title: HSC TKO rep1


title: HSC P110d rep3

value: Pik3calox-lox; Pik3cblox-lox;Pik3cd-/-


title: FTW-ESC.r2.H3K4me3

description: Mouse FTW-embryonic stem cell, repeat2, H3K4me3 (ChIP-seq)

value: FTW-embryonic stem cell

tag: antibody


title: FTW-ESC.r2.input

description: Mouse FTW-embryonic stem cell, repeat2, Input DNA (ChIP-seq)

value: Input DNA


title: INPUT_w1118_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G11_AD008

value: brain

value: ACA

value: TH


title: HSC P110d rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G11_AD001

value: MOp

value: SSp


title: FTW-ESC.r1.H3K27me3

description: Mouse FTW-embryonic stem cell, repeat1, H3K27me3 (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD012


title: INPUT_w1118_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: whole brain


title: HSC P110d rep1

value: Bone


title: RIP_CG6422_Fmr1_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: DRG KO Mouse 6

first: Wendy

middle: Marie

last: Campana

address: 9500 Gilman Drive

department: Anesthesiology

institute: University of California San Diego

data_processing:
Sequencing reads were trimmed using Trimmomatic v0.38 using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27
Reads were aligned to GRCm38 using STAR v2.6.0a and quantified using RSEM 1.3.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts matrix

source_name: Dorsal root ganglion

extract_protocol:
Total RNA was extracted from 3 GluN1+ and 3 GluN1- DRGs collected at the L3-L4 level.  Total RNA was extracted in Trizol® and purified using the Nucleospin RNA kit (Macherey-Nagel).    RNA was assessed for quality using an Agilent Tapestation 4200; samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NMDA-R Knockout

value: Schwann cells


title: FTW-ESC.r1.H3K4me3

description: Mouse FTW-embryonic stem cell, repeat1, H3K4me3 (ChIP-seq)


title: FTW-ESC.r2.H3K27me3

description: Mouse FTW-embryonic stem cell, repeat2, H3K27me3 (ChIP-seq)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G10_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G11_AD012


title: INPUT_CG6422_REP7

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: DRG KO Mouse 5


title: FTW-ESC.r1.input

description: Mouse FTW-embryonic stem cell, repeat1, Input DNA (ChIP-seq)


title: DRG KO Mouse 4


title: INPUT_CG6422_REP3

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: CeA, MG Depletion/Dep #29

description: MG Depletion/Dep #29 CeA abundance

source_name: central nucleus of the amygdala

value: central nucleus of the amygdala

value: post-natal day 119

tag: chow

value: Dependent (Dep)


title: INPUT_CG6422_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P1_180801_P2_G11_AD010

value: male


title: INPUT_w1118_REP5

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

value: wild type


title: FTW-ESC#2.r2.RNA-seq

description: Mouse FTW-embryonic stem cell#2, repeat2, RNA-seq


title: INPUT_w1118_REP2

description:
R1: Read; R2: UMI
rawcounts_genes.tsv


title: DRG WT Mouse 3

value: Wildtype


title: FTW-ESC#2.r1.RNA-seq

description: Mouse FTW-embryonic stem cell#2, repeat1, RNA-seq

value: FTW-embryonic stem cell


title: DRG WT Mouse 2


title: CeA, MG Depletion/Dep #07

description: MG Depletion/Dep #07 CeA abundance

tag: ethanol exposure


title: CeA, MG Depletion/Dep #08

description: MG Depletion/Dep #08 CeA abundance


title: FTW-ESC#1.r2.RNA-seq

description: Mouse FTW-embryonic stem cell#1, repeat2, RNA-seq


title: CeA, MG Depletion/Dep #06

description: MG Depletion/Dep #06 CeA abundance


title: FTW-ESC#1.r1.RNA-seq

description: Mouse FTW-embryonic stem cell#1, repeat1, RNA-seq


title: SpleenNon-TFH2

data_processing:
Illumina’s RTA software used for basecalling.
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark collection of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10

source_name: Spleen CD4+ T cells

extract_protocol:
Single cells from lung or spleen were isolated, and RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

tag: cell markers

tag: infection

value: Influenza A/PR8/34 (28 d.p.i.)


title: m11b_3

city: San Francisco

first: Matthew

last: Krummel

state: CALIFORNIA

address: 513 Parnassus Ave, UCSF, Dept. of pathology, HSW518

institute: UCSF

data_processing:
STAR 2.4.2a was used to align reads to the Mus Musculus genome, version GRCm38.78
Only mapped reads uniquely assigned to the mouse genome were used for differential expression testing.  These were imported into R and then converted to normalized read counts with DESeq2
QC plots were created from the counts generated by DESeq2’s variance Stabilizing Transformation (with blind=True).
Differential Expression was performed using DESeq2, and significant genes were filtered by a q-value (False Discovery Rate) threshold of 0.05, and a p-value threshold of 0.05.
Genome_build: GRCm38.78
Supplementary_files_format_and_content: czv, read count, fold change

source_name: OTI T cells

growth_protocol: OTI T cells were incubated with antigen bearing DC subsets for 72 hours in 96 well V bottom plates in RPMI + 10% FBS + PSG + beta-mercaptoethanol

extract_protocol:
Divided OTI T cells were flow sorted into lysis buffer
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: CD8+ T cells

tag: dc partner

value: Migratory CD11b+ DC


title: SpleenTFH2

tag: tissue


title: CeA, Control Diet/Dep #09

description: Control Diet/Dep #09 CeA abundance

tag: age

value: Control Diet


title: A549_siPLANE_1

city: Zhengzhou

first: liu

last: Teng

address: No 7,Weiwu Road,Jinshui  District

department: Translational Research Institute

institute: Henan Provincial People’s Hospital and People’s Hospital of Zhengzhou University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file includes counts and  FPKM values for each Sample

source_name: Lung adinocarcinoma cell  line

growth_protocol: cells were maintained in DMEM (Biological Industries, #01-052-1ACS; Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS, Biological Industries, #04-001-1A; Beit Haemek, Israel) and 1% penicillin-streptomycin (Biological Industries, #03-031-1BCS，Beit Haemek, Israel).  Cells were cultured in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol™ Reagent(Catalog number:  15596026,ThermoFisher Scientific) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were seeded in 6-well plate (1.5X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000-015) according to the manufacturer’s instructions.

tag: cell line

value: transfected with  PLANE siRNA

value: PLANE knockdown


title: A549_siPLANE_2


title: Bko2

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

description: processed data file: B_rawcounts.txt

data_processing:
Library strategy: DNA sequencing
The sequencing reads of sgRNAs from different samples were first identified by barcode using cutadapt (version 1.11) with parameters –u (43, -87 for R1; 73, -57 for R2).
Bowtie2-build function of Bowtie2 (version 2.3.4.3) (Langmead and Salzberg 2012) was applied on the sgRNA sequences of GeCKO library to generate Burrows-Wheeler index. The sgRNA sequences were then retrieved and counted by aligning processed reads of each sample to the sgRNA library using Bowtie2 with default parameters and only the reads with unique alignment were reported.
The MAGeCK algorithm was used to estimate the statistical significant (using a negative binomial test) of enrichment for each gRNA in the KO-screened group compared to control group.
Genome_build: The sgRNAs sequences were from GeCKO library and could be download from
Supplementary_files_format_and_content: *_rawcounts.txt: Tab-delimited text files include raw counts.

source_name: human embryonic stem cells

growth_protocol: hPSCs were cultured in medium (DMEM/F12, KOSR, NEAA, β-Me, FGF2). hPSCs were cultured at 37 ℃ and 5% CO2 on feeder layer growth-arrested mouse embryonic fibroblasts (MEFs) in standard hESC growth medium, composed of DMEM/F12 with 20% Knockout Serum Replacement (KOSR),1x L-Glutamine,1x nonessential amino acids(NEAA), 0.1 mM β-mercaptoethanol and 4 ng ml-1 basic fibroblast growth factor (bFGF). Cells were passaged every 5 days with dispase digestion.

extract_protocol:
Genomic DNA of sorted cells was extracted with quickExtract DNA Extraction Solution (Epicentre, QE09050) and the sgRNAs were amplified by two-step PCR method.
For the second PCR, illumine adaptors and barcode were attached to samples. Amplicons from the second PCR were gel-extracted, quantified, mixed and sequenced using pair-ended 150bp sequencing protocol (Illumina Hiseq-x-ten system).

treatment_protocol: A total of 10 million PAX6-tdTomato/iCas9 hPSCs were transduced with each virus library at a multiplicity of infection (MOI) of 0.3, resulting in infection of 30% of the cells and hence leading to a 50-fold coverage of the sgRNA library size. After culturing at 37 ℃ for about 1.5 h, the transduced cells were plated on 6 six-well plates of MEF layer. At 24 h after transduction, cells were treated with puromycin (0.5 μg/ml) for 4 days to eliminate non-infected cells. Then doxycycline (Dox) were added to 5 six-well plates for 5 days, that one plate left without Dox treatment was as control. The cells with or without Dox treatment were passaged at a ratio of 1:5. Another 7 days later, the cells were digested with preheated trypsin to create a single cell suspension and tdTomato-positive cells were collected by FASC sorting (BD FACSVerse™ System, BD Biosciences). The wide-type ESCs and infected iCas9 ESCs without Dox treatment were as control cells.

value: Embryonic stem cells

tag: time point

value: Day 17

tag: genotype/variation

value: pooled mutant cells


title: A549_NC_1

value: transfected with  negtive control siRNA

tag: genotype

value: control


title: CeA, Control Diet/Dep #11

description: Control Diet/Dep #11 CeA abundance

value: central nucleus of the amygdala

value: post-natal day 119

value: Dependent (Dep)


title: CD8a_2

value: LN resident CD8a+ DC


title: Bko1

description: processed data file: B_rawcounts.txt


title: CeA, Control Diet/Dep #02

description: Control Diet/Dep #02 CeA abundance


title: CeA, Control Diet/Dep #03

description: Control Diet/Dep #03 CeA abundance


title: SpleenTFH1


title: m11b_2


title: CD8a_3


title: CeA, Control Diet/Dep #01

description: Control Diet/Dep #01 CeA abundance


title: INPUT_CG6422_REP1

description:
R1: Read; R2: UMI
rawcounts_genes.tsv

tag: stock

value: whole brain

tag: ip


title: LungNon-TTH2

source_name: Lung CD4+ T cells

value: Lung


title: DRG WT Mouse 1

value: Wildtype

tag: cell type

value: Schwann cells


title: Bpool

description: processed data file: B_rawcounts.txt


title: CD8a_1

value: CD8+ T cells


title: A549_NC_2

tag: treatment


title: LungNon-TTH1

value: Influenza A/PR8/34 (28 d.p.i.)


title: SpleenNon-TFH1

value: Spleen


title: CD103_3

value: Migratory CD103+ DC


title: CeA, MG Depletion/Non-Dep #47

description: MG Depletion/Non-Dep #47 CeA abundance

value: Non-Dependent (Non-Dep)


title: Ako2

description: processed data file: A_rawcounts.txt

value: Embryonic stem cells

value: Day 17


title: LungTTH2


title: CeA, MG Depletion/Non-Dep #46

description: MG Depletion/Non-Dep #46 CeA abundance


title: Ako1

description: processed data file: A_rawcounts.txt

value: pooled mutant cells


title: CD103_2


title: Apool

description: processed data file: A_rawcounts.txt


title: CeA, MG Depletion/Non-Dep #23

description: MG Depletion/Non-Dep #23 CeA abundance


title: CD103_1


title: MitoS3.B -48h R2

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

data_processing:
Reads were aligned to mouse transcriptome (Mus musculus transcriptome generated by rsem-prepare-reference with ENSEMBL93 GTF) and mouse genome (GRCm38.p6) using HISAT2 v. 2.1.0. Gene expression levels were quantified with RSEM v. 1.3.1 using transcriptome alignments.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text RSEM output files including for each sample: gene_id, transcript_id(s), length, effective_lenght, expected_count, TPM, FPKM.

source_name: MitoS3.B -48h_mESCs

growth_protocol: Mouse ES cells were cultured without feeders on gelatine-coated plates (0.2% gelatine) in serum-free KSR-based medium (Life Technologies) supplemented with: 1 μM PD0325901, 3 mM CHIR99021 (2i); and 100 units/m LIF (2iLIF).

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse ES cells stabilized in 2iLIF were cultured in absence of 2iLIF for 48 hours to mimic differentiation process.

tag: strain background

value: mouse embryonic stem cell

value: Stat3 knock-out expressing MLS-NES-Stat3 construct (clone B)

tag: phenotype

value: adherent

tag: growth condition

value: without 2iLIF for 48 hours


title: CeA, MG Depletion/Non-Dep #13

description: MG Depletion/Non-Dep #13 CeA abundance

data_processing:
Adapters were trimmed and filtered using tagseq_clipper.pl and tagseq_trim_launch.pl https://github.com/z0on/tag-based_RNAseq
Raw 3'UTR biased-sequencing files were evaluated for quality control using FastQC (0.11.8).
Reads were mapped to the mouse reference genome (UCSC, mm10) using the alignment tool Bowtie2 (v2.3.4.3).
HTSeq (v.0.11.0), was used for counting mapped sequencing reads.
Quantified read counts were normalized and analyzed for differential expression using DESeq2 (v 1.10.1), between microglia intact and microglia depleted animals, within the R statistical computing environment (v3.5.1)
Genome_build: GRCm38.p6.genome.fa.gz from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

extract_protocol:
medial prefrontal cortex was fresh dissected, flash frozen on dry ice.The remainder of the brain was flash frozen in OCT and sliced at 300um. The CeA was then punched and the RNA from each region was isolated using Trizol reagent and MagMAX-96 Total RNA Isolation Kit . DNA contamination removed using DNA-free kit.  (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA was fragmented then first strand synthesis occurred using majority deoxycytidine nucleotides which served as an anchor for the switch oligos. swOligo used: /5Me-isodC/iisodG/iMeisodC/CCATGCGGCTACACGACGC TCTTCCGATCTNNMWrGrGrG. cDNA strand with portions of adapter were added then amplified, followed by second PCR to add index portion of the adapter.
Samples were then pooled, size selected with Pippin then sequenced on a Single End Run using the HiSeq 2500 for mPFC and NovaSeq 6000 for CeA for a read depth of ~4 million reads per sample

value: central nucleus of the amygdala

value: post-natal day 119

tag: chow

tag: ethanol exposure


title: MitoS3.B -48h R1


title: MitoS3.A -48h R2

source_name: MitoS3.A -48h_mESCs

value: Stat3 knock-out expressing MLS-NES-Stat3 construct (clone A)


title: CeA, Control Diet/Non-Dep #20

description: Control Diet/Non-Dep #20 CeA abundance

tag: strain

value: Control Diet


title: CeA, Control Diet/Non-Dep #19

description: Control Diet/Non-Dep #19 CeA abundance


title: CeA, Control Diet/Non-Dep #17

description: Control Diet/Non-Dep #17 CeA abundance


title: MILI IP;P0;Tex15+/- [RR559]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
RR559
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

data_processing:
Reads were sorted into individual libraries based on the barcodes, the 3' adapter sequences were removed and mapped to the mouse genome (mm10). The software used for processing the data (genomic coordinates, etc.) from the raw data files were in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GEO_tex15_mappers.csv.gz: The file contains mapping of the reads corresponding to individual small RNAs to mouse genome (mm10).

source_name: testes

growth_protocol: To analyze the function of Tex15 throughout the spermatogenesis, the knock-out mouse of the Tex15 was prepared.

extract_protocol:
Total small RNAs were isolated from E16.5 embryos. Briefly, total RNA from E16.5 testes was separated on 15% UREA polyacrylamide gel. The gel was cut between 16-40 nts to isolate total small RNAs. RNAs present in endogenous MILI, and MIWI2, complexes were isolated. Briefly, immunoprecipitations were treated with Proteinase K in 300 μl reaction at 42 °C for 15 min (10 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% SDS). RNAs present in the sample were purified by phenol-chloroform extraction and precipitated with ethanol. Approximately 10-20% of the sample was labelled at the 5′ end with polynucleotide kinase (PNK, ThermoFisher Scientific) and [γ 32P] ATP (3000 Ci/mmol, Perkin Elmer), and resolved by 15% urea-PAGE for quality check.
Libraries were prepared (barcoded at 3′ end) using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB Catalogue No. E7300) following manufacturer instructions. The synthesized cDNA libraries were resolved on 3% high-resolution MethaPhor agarose (Lonza, cat. No. 50180) gels in TAE buffer. Fragments in the size-range of ~160 bp were gel-extracted with the use of MinElute Gel Extraction Kit (Qiagen, cat No. 28604). Multiple libraries with different barcodes (at 3′ end) were mixed in equimolar ratios and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg).

value: testes

tag: gender

value: male

tag: purification

value: MILI IP

tag: ip antibody

value: MILI (mouse monoclonal) (Reuter et al., 2009; PMID:19465913)


title: S3-/- -48h R2

value: Stat3 knock-out


title: MILI IP;P0;Tex15+/- [RR558]

description:
RR558
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

tag: tissue

tag: age


title: MitoS3.A -48h R1

tag: genotype/variation