title: emx_ctrl_77ctx2

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description:
processed data file:
emx.cntTable.txt
gene_count_matrix_2.csv
fullMMERVK10C_count_matrix_2.csv
ERVK_count_matrix_2.csv
TE_count_matrix_2.csv

data_processing:
Unique mapping - RNAseq (STAR aligner (2.6.0))
Quantification of reads mapping to genes - RNAseq (featureCounts from Subread (1.6.3))
Quantification of reads mapping to TEs - RNAseq (featureCounts from Subread (1.6.3))
Quantification of reads mapping to ERVKs- RNAseq (featureCounts from Subread (1.6.3))
Quantification of reads mapping to full MMERVK10C - RNAseq (featureCounts from Subread (1.6.3))
Multi mapping - RNAseq (STAR aligner (2.6.0))
Quantification of reads mapping to genes and TE subfamilies - RNAseq (TEtranscripts from TEToolkit (2.0.3))
Base calling, demultiplexing and convertion to fastq - single cell (cellranger mkfastq (3.0))
Read quantification - single cell (cellranger count (3.0))
Unique mapping - Cut and run (Bowtie2 (2.3.4.2))
Subtraction of input signal - Cut and run (BamCompare from deeptools)
Compute mean of signals for the different guide RNAs - RNAseq (invitro CRISPR NPC)
computeMatrix for plotHeatmap of full length MMERVK10C elements (deeptools) - RNAseq (invitro CRISPR NPC) and Cut and Run
Genome_build: GRCm38.p6 vM19
Supplementary_files_format_and_content: counts matrix; binary count matrix for CR020_S9 and CR021_S10

growth_protocol: In vitro CRISPR: NPC cultures from Rosa26-Cas9 knock-in transgenic mice (embryonic day 13.5). The forebrain was mechanically dissociated and plated in gelatin coated flasks and maintained as a monolayer culture in NSA medium (Euromed, Euroclone) supplemented with N2 hormone mix, EGF (20 ng/ml; Gibco), bFGF (20 ng/ml; Gibco), 2 nM L-glutamine and 100 ug/ml Pen/Strep. Cells were then passaged 1:3-1:6 every 2-3 days using Accutase (Gibco).

extract_protocol:
In vitro CRISPR: Cells were detached and resuspended in basic culture media (media excluding growth factors) with propidium iodide (1:1,000; BD Biosciences) and strained (70 mm filters, BD Biosciences). RFP+ cells were FACS isolated at 4°C (reanalysis showed >99% purity) and pelleted at 1,500 rpm for 5 min, snap frozen on dry ice and stored at -80°C until RNA/DNA were isolated. For all in vivo CRISPR experiments animals were sacrificed after two months and analyzed either by IHC or nuclei isolation (see details below) followed by DNA- or RNA-seq. Emx animals (RNAseq): Animals were sacrificed at 3 months of age for either immunohistochemistry IHC or RNA sequencing. Emx animals (single cell): The nuclei isolation was performed according to Sodersten et al. (2018). The tissue was thawed and dissociated in ice-cold lysis buffer ((0.32 M sucrose, 5 mM CaCl2,  3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8  M sucrose, 3  mM MgAc, 10  mM Tris-HCl, pH 8.0, and 1 1 mM DTT) before centrifugation at 30,000 ×  g  for 2 hours and 15 min. Pelleted nuclei were softened for 10 minutes in 100 ml of nuclear storage buffer (15% sucrose, 10  mM Tris-_HCl, pH 7.2, 70  mM KCl, and 2  mM MgCl2) before resuspended in 300 ml of dilution buffer (10  mM Tris-_HCl, pH 7.2, 70  mM KCl, and 2  mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C with low flowrate using a 100 mm nozzle (reanalysis showed >99% purity).
RNAseq: Total RNA was isolated from frozen cell/nuclei pellets and brain tissue using the RNeasy Mini Kit (Qiagen) and used for RNA-seq and qPCR (tissue pieces were run in the tissue lyser for 2 min, 30 Hz, prior to RNA isolation). Single cell: 8,500 nuclei per sample were sorted via FACS and loaded onto 10X Genomics Single Cell 3’ Chip along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Single Cell 3′ Library (10X Genomics, PN-120233) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics and sequencing libraries were generated with unique sample indices (SI) for each sample.
RNAseq libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2 × 150bp). Cut and run (IgG and H3K9me3) library preparation was performed using the Hyper prep kit (KAPA biosystems) and sequenced on NextSeq500 2 x 75 bp. For the single cell sequencing, libraries for samples were multiplexed and sequenced on a Novaseq using a 150-cycle kit.

treatment_protocol: In vitro CRISPR: Transduced with a lentiviral vector expressing gRNAs (LV.gRNAs) designed to target either exon 3, 4 or 13 of Trim28 or to target lacZ as well as a nuclear RFP reporter gene (H2B-RFP). Lentiviruses were produced according to Zufferey et al  and titers were 10^9 TU/ml, which was determined using qRT-PCR. Cas9 mouse NPCs where transduced at a MOI 40 and allowed to expand for 10 days prior to FACS. In vivo CRISPR Trim28fl: AAV vectors expressing Cre were injected into the forebrain of adult floxed Trim28 animals. The production of AAV5 vectors has been described in detail elsewhere (Ulusoy et al 2009)  and titers were in the order of 1013 TU/ml, which was determined by qRT-PCR using taqman primers towards the ITR . Prior to injection, the vectors were diluted in PBS; the vectors containing the guide RNAs were diluted to 30% except upon co-injection of guides 3, 4, and 13 where the vectors were diluted to 10% each. Rosa26 Cas9 knock-in mice where anesthetized by isoflurane prior to the intra-striatal injections (coordinates from bregma: AP +0.9 mm, ML +1.8 mm, DV -2.7 mm) of 1 ml virus solution (0.1 µl/15 s). The needle was kept in place for additional 2 min post injection to avoid backflow. In vivo CRISPR Cas9: We used AAV vectors to express guides 3, 4 and 13 (targeting exon 3, 4 and 13 of Trim28) and H2B-RFP under Synapsin. The production of AAV5 vectors has been described in detail elsewhere (Ulusoy et al 2009)  and titers were in the order of 10^13 TU/ml, which was determined by qRT-PCR using taqman primers towards the ITR . Prior to injection, the vectors were diluted in PBS; the vectors containing the guide RNAs were diluted to 30% except upon co-injection of guides 3, 4, and 13 where the vectors were diluted to 10% each. Rosa26 Cas9 knock-in mice where anesthetized by isoflurane prior to the intra-striatal injections (coordinates from bregma: AP +0.9 mm, ML +1.8 mm, DV -2.7 mm) of 1 ml virus solution (0.1 µl/15 s). The needle was kept in place for additional 2 min post injection to avoid backflow. In vivo CRISPR Stop Cas9: We generated AAV-vectors expressing the gRNAs and a Cre-inducible H2B-RFP reporter, as well as an AAV-vector expressing Cre under the control of the neuron-specific Synapsin  (SYN) promoter. The production of AAV5 vectors has been described in detail elsewhere (Ulusoy et al 2009)  and titers were in the order of 10^13 TU/ml, which was determined by qRT-PCR using taqman primers towards the ITR . Prior to injection, the vectors were diluted in PBS; the vectors containing the guide RNAs were diluted to 30% except upon co-injection of guides 3, 4, and 13 where the vectors were diluted to 10% each. Rosa26 Cas9 knock-in mice where anesthetized by isoflurane prior to the intra-striatal injections (coordinates from bregma: AP +0.9 mm, ML +1.8 mm, DV -2.7 mm) of 1 ml virus solution (0.1 µl/15 s). The needle was kept in place for additional 2 min post injection to avoid backflow. Cut and Run (IgG and H3K9me3): The Cut & Run were performed according to Skene et al 2018 . In brief, 200.,000 mouse NPCs were washed, permeabilized and attached to ConA-coated magnetic beads (Bang Laboratories) before incubated with the H3K9me3 (1:50, ab8898,  Abcam) antibody at 4°C overnight. Cells were washed and incubated with pA-MNase fusion protein and digestion was activated by adding CaCl2  at 0°C. The digestion was stopped after 30 min and the target chromatin released from the insoluble nuclear chromatin before extracting the DNA. Emx animals (single cell): Animals were sacrificed by cervical dislocation and brains quickly removed. The desired regions were dissected and snap frozen on dry ice and stored at -80°C.

tag: experiment

value: Emx animals

tag: condition

value: Control

value: Male Emx1-Cre (+/-); Trim28-fl (+/-); gtRosa(+/-) were bred with Trim28-fl (+/+) females to generate animals in which one (Emx1-Cre +/-; Trim28-fl+/-) or both (Emx1-Cre +/-; Trim28-fl +/+) Trim28 alleles had been excised, used as control and Trim28-KO, respectively.


title: Maternal_blood_NonTD_26

status: Public on Feb 24 2021

type: RNA

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

country: USA

institute: UC Davis

description: nutrient metabolites: Y: yes, we have metabolites data for that sample; N: no, we don't have metabolites data for that sample.  Nutrient metabolites information is included in the paper supplementary tables. There are multiple metabolites and different samples have different metabolites, as detailed in the paper methods and supplementary tables.

hyb_protocol: Biotin-labeled cRNA was hybridized to Human Gene 2.0 array (Affymetrix) at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol

scan_protocol: Hybridized arrays were scanned at the John's Hopkins Sequencing and Microarray core. The manufacturer’s protocol was followed for all washing, staining and scanning procedures.

data_processing: Robust Multi-Chip Average (RMA) in oligo R package was used for data normalization using Affymetrix CEL files. For the quality control, we used oligo and ArrayQualityMetrics R packages. No samples were identified as outliers with principal component analysis, Kolmogorov-Smirnov test and distances to other arrays analysis. Probes were mapped to the transcripts and genes using pd.hugene.2.0.st R package on 36,459 probes.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Total RNA with RIN > 7 was converted cDNA and in vitro transcribed to biotin-labeled cRNA at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol (Affymetrix)

extract_protocol: Maternal peripheral blood was collected at study visits during all three trimesters of pregnancy in PAXgene Blood RNA tube with the RNA stabilization reagent (BD Biosciences) and stored frozen at -80°C. RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. Total RNA was converted to cDNA and biotin labeled. Expression was measured using Human Gene 2.0 Affymetrix microarray chips by the John Hopkins Sequencing and Microarray core following by washing, staining and scanning procedures based on manufacture’s protocol.

tag: diagnosis

value: NonTD

tag: Sex

value: F

tag: study

value: MARBLES

tag: array batch

tag: nutrient metabolites

value: Y


title: Maternal_blood_NonTD_19

value: M


title: RNA-seq_D3_MDDCs_Pam3CSK4

type: SRA

city: Dallas

first: Edward

last: Wakeland

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2.17.04 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and mapped to hg19 whole genome using CLC-Bio Genomics Workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC-Bio Genomics Workbench.
Genome_build: hg19

source_name: Human monocyte-derived dendritic cells

growth_protocol: Human monocytes were cultured in RPMI-1640 medium with 10% FBS, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 100U/ml penicillin, and 100 µg/mL streptomycin. To differentiate monocytes into macrophages or dendritic cells, recombinant human M-CSF (50ng/mL) or recombinant human GM-CSF (100ng/mL) and recombinant human IL-4 (50ng/mL) were used, respectively. The culture medium which contained fresh recombinant human M-CSF or recombinant human GM-CSF and recombinant human IL-4 was replaced every 2 days.

extract_protocol:
RNA was extracted using TRIzol reagent and RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Monocytes, MDMs or MDDCs were stimulated with Pam3CSK4 (1 μg/ml), LPS (10 ng/ml), R837 (10 μg/ml) or R848 (10 μg/ml) for 18 hours.

tag: cell type

value: Human monocyte-derived dendritic cells

tag: donor

value: Donor 3

tag: treatment


title: CR020_S9

description:
processed data file:
mm10_fullMMERVK10C_H3K9me3_Trim28_stranded50.means.mat

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: IgG

value: Goat pAb to Rb IgG; Abcam, Ab97047, GR254157-16


title: Maternal_blood_NonTD_21


title: Maternal_blood_NonTD_20


title: CR021_S10


title: DIF_TAM_RNAPII_A

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

data_processing:
The FASTQ files were mapped to the mouse reference genome (assembly mm9) using BOWTIE2 with very-sensitive presets in end-to-end mode. The resulting BAM files of ChIPs were deduplicated and MAPQ >2 filtered using Samtools. The corresponding BAM files of the replicates were merged within condition. The merged BAM files were normalized to 1x genomic content (RPGC) using the bamCoverage function of Deeptools.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig represent the normalized reads per genomic content (RPGC) values of ChIP-seq signal

growth_protocol: Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S

extract_protocol:
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. 1µg antibody was used for immunoprecipitation. After reversing the cross-linking, the DNA was isolated by phenol-chloroform-isoamyl extraction.
Libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions

treatment_protocol: For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).

tag: strain background

tag: genotype/variation

value: Mutant RNF40RosaCreERT2 mouse

value: Primary Calvarial Osteoblasts

value: for 7 d with 250nm 4-hydroxytamoxifen, and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate

tag: chip antibody

value: RNAPII (N-20), Santa Cruz sc-899

tag: molecule subtype

value: ChIP DNA


title: RNA-seq_D3_MDDCs_unstimulated

value: NT


title: Maternal_blood_NonTD_18


title: RNA-seq_D3_MDMs_R848

source_name: Human monocyte-derived macrophages

value: Human monocyte-derived macrophages


title: Maternal_blood_NonTD_15


title: negative control

city: Houston

first: Weiyi

last: Peng

state: Texas

address: 3517 Cullen Blvd, Room 3025

institute: University of Houston

data_processing:
The reads were mapped to mouse mm10+gencodevM14 using HiSAT2/2.1.0.
stringtie/1.3.0 were used to calculate the gene expressions. preDE.py was used to count the reads.
edgeR were used to do differential expression analysis
GSEA were applied to logFC ranked genes
Genome_build: mm10+gencodevM14
Supplementary_files_format_and_content: differential expression analysis results in Excel file

source_name: MC38/gp100 murine cancer cell line

extract_protocol:
Cell lines were washed and RNAs were harvested using Qiagen RNeasy Plus kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Non-treament

tag: cell line


title: DIF_VEH_H2Bub1_B

value: for 7 d with vehicle(ethanol) and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate

value: H2Bub1 (D11), Cell Signaling #5546


title: emx_ctrl_65ctx2

value: Emx animals

value: Control

value: Male Emx1-Cre (+/-); Trim28-fl (+/-); gtRosa(+/-) were bred with Trim28-fl (+/+) females to generate animals in which one (Emx1-Cre +/-; Trim28-fl+/-) or both (Emx1-Cre +/-; Trim28-fl +/+) Trim28 alleles had been excised, used as control and Trim28-KO, respectively.


title: emx_ctrl_64ctx2


title: Maternal_blood_NonTD_16

value: NonTD

value: M

value: MARBLES

value: Y


title: emx_ko_76ctx2

value: KO


title: DIF_VEH_H2Bub1_A

value: Mutant RNF40RosaCreERT2 mouse


title: Maternal_blood_NonTD_14

value: F


title: DIF_TAM_H2Bub1_A

value: Primary Calvarial Osteoblasts

value: for 7 d with 250nm 4-hydroxytamoxifen, and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate


title: Maternal_blood_NonTD_13


title: RNA-seq_D3_MDMs_Pam3CSK4

value: Donor 3


title: RNA-seq_D3_MDMs_R837


title: DIF_TAM_H2Bub1_B

value: ChIP DNA


title: RNA-seq_D3_MDMs_LPS

value: Human monocyte-derived macrophages


title: emx_ko_73ctx2


title: emx_ko_60ctx2


title: Maternal_blood_NonTD_17


title: invivo_crispr_ko_stopcas_g4

description:
processed data file:
invivo_crispr_cas_stopcas.cntTable.txt
gene_count_matrix_2.csv
fullMMERVK10C_count_matrix_2.csv
ERVK_count_matrix_2.csv
TE_count_matrix_2.csv

value: In vivo CRISPR Stop Cas9

tag: guide (if applicable)

value: Stop-Cas9-GFP knock-in mice


title: invivo_crispr_ctrl_stopcas_ctrl


title: Maternal_blood_NonTD_23


title: Maternal_blood_NonTD_22


title: RNA-seq_D3_MDMs_unstimulated

value: NT


title: Adult medulloblastoma sample N26

type: genomic

city: Bonn

first: Tobias

last: Goschzik

address: Venusberg-Campus 1

department: Neuropathology

institute: University of Bonn Medical Center

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip (850K) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Average Beta
Unmethylated and methylated signal intensities

source_name: FFPE-DNA from N26

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE tumor samples using Qiagen QIAamp FFPE DNA tissue kit according to manufacturer's instructions

tag: disease

value: Adult medulloblastoma

tag: gender

value: female


title: RNA-seq_D3_mono_R848

source_name: Human monocytes

value: Human monocytes


title: Adult medulloblastoma sample N25

source_name: FFPE-DNA from N25

value: male


title: Adult medulloblastoma sample N24

source_name: FFPE-DNA from N24


title: Adult medulloblastoma sample Sm1

source_name: FFPE-DNA from Sm1


title: RNA-seq_D3_mono_LPS


title: Adult medulloblastoma sample N23

source_name: FFPE-DNA from N23


title: Adult medulloblastoma sample N22

source_name: FFPE-DNA from N22


title: RNA-seq_D3_mono_Pam3CSK4


title: Maternal_blood_NonTD_12

value: NonTD

value: M

value: MARBLES


title: invivo_crispr_ko_cas_g4

tag: experiment

value: In vivo CRISPR Cas9

tag: condition

value: KO

value: Cas9 GFP knock-in mice


title: invivo_crispr_ko_stopcas_g13


title: Maternal_blood_NonTD_10

tag: diagnosis

tag: Sex

value: F

value: Y


title: Maternal_blood_NonTD_9

tag: study

tag: array batch


title: Maternal_blood_NonTD_11

tag: nutrient metabolites


title: Adult medulloblastoma sample N20

source_name: FFPE-DNA from N20


title: invivo_crispr_ko_stopcas_g3g4g13


title: Adult medulloblastoma sample N21

source_name: FFPE-DNA from N21


title: RNA-seq_D2_MDDCs_R848

tag: cell type

value: Human monocyte-derived dendritic cells

tag: donor

value: Donor 2


title: Adult medulloblastoma sample N19

source_name: FFPE-DNA from N19


title: Maternal_blood_NonTD_8


title: Maternal_blood_NonTD_6

value: N


title: invivo_crispr_ko_stopcas_g3

value: In vivo CRISPR Stop Cas9

value: Stop-Cas9-GFP knock-in mice


title: Maternal_blood_NonTD_4


title: invivo_crispr_ko_cas_g3g4g13


title: RNA-seq_D3_mono_R837

value: Donor 3

tag: treatment


title: invivo_crispr_ko_cas_g3

tag: genotype/variation


title: RNA-seq_D2_MDDCs_LPS


title: invivo_crispr_ko_cas_g13


title: RNA-seq_D2_MDDCs_Pam3CSK4


title: Adult medulloblastoma sample N18

source_name: FFPE-DNA from N18

value: Adult medulloblastoma


title: Maternal_blood_NonTD_5


title: Maternal_blood_NonTD_7


title: Maternal_blood_NonTD_3


title: invivo_crispr_ctrl_cas_ctrl

value: Control


title: Maternal_blood_NonTD_2


title: RNA-seq_D2_MDDCs_unstimulated

value: NT


title: Adult medulloblastoma sample N17

source_name: FFPE-DNA from N17

value: male


title: RNA-seq_D2_MDMs_R837

value: Human monocyte-derived macrophages


title: RNA-seq_D3_mono_unstimulated

value: Human monocytes


title: Adult medulloblastoma sample N16

source_name: FFPE-DNA from N16

value: female


title: Adult medulloblastoma sample N15

source_name: FFPE-DNA from N15


title: invivo_crispr_ko_trim28fl_796

description:
processed data file:
invivo_crispr_trim28fl.cntTable.txt
gene_count_matrix_2.csv
fullMMERVK10C_count_matrix_2.csv
ERVK_count_matrix_2.csv
TE_count_matrix_2.csv

value: In vivo CRISPR Trim28fl

value: KO

value: Trim28 floxed mice


title: RNA-seq_D2_MDMs_LPS


title: Maternal_blood_ASD_56

value: ASD

value: M

value: MARBLES

value: Y


title: invivo_crispr_ko_trim28fl_823


title: Adult medulloblastoma sample N12

source_name: FFPE-DNA from N12


title: Adult medulloblastoma sample N13

source_name: FFPE-DNA from N13


title: Maternal_blood_NonTD_1

value: NonTD

value: N


title: RNA-seq_D2_MDMs_unstimulated

source_name: Human monocyte-derived macrophages

value: Donor 2


title: Adult medulloblastoma sample N11

source_name: FFPE-DNA from N11

value: Adult medulloblastoma


title: RNA-seq_D2_mono_R848

source_name: Human monocytes


title: RNA-seq_D2_MDMs_R848


title: Adult medulloblastoma sample N10

source_name: FFPE-DNA from N10


title: invivo_crispr_ko_trim28fl_795


title: Adult medulloblastoma sample N14

source_name: FFPE-DNA from N14


title: Maternal_blood_ASD_55


title: invivo_crispr_ko_trim28fl_794


title: Maternal_blood_ASD_53


title: npc_ctrl_842

description:
processed data file:
npc.cntTable.txt
gene_count_matrix_2.csv
fullMMERVK10C_count_matrix_2.csv
ERVK_count_matrix_2.csv
TE_count_matrix_2.csv

value: In vitro CRISPR

value: Control

value: Rosa26-Cas9 knock-in mice


title: npc_ko_g13_876


title: invivo_crispr_ctrl_trim28fl_822


title: RNA-seq_D2_MDMs_Pam3CSK4

value: Human monocyte-derived macrophages


title: invivo_crispr_ctrl_trim28fl_799


title: Maternal_blood_ASD_46


title: Maternal_blood_ASD_51

value: F


title: Maternal_blood_ASD_47


title: RNA-seq_D2_mono_LPS

value: Human monocytes


title: Maternal_blood_ASD_52


title: Adult medulloblastoma sample N07

source_name: FFPE-DNA from N07

value: male


title: invivo_crispr_ctrl_trim28fl_797

value: In vivo CRISPR Trim28fl


title: Adult medulloblastoma sample N09

source_name: FFPE-DNA from N09

value: female


title: Adult medulloblastoma sample N05

source_name: FFPE-DNA from N05


title: Maternal_blood_ASD_50

value: ASD


title: Maternal_blood_ASD_45

value: M


title: npc_ctrl_867


title: Maternal_blood_ASD_49

value: MARBLES


title: Maternal_blood_ASD_44

value: Y


title: Adult medulloblastoma sample N04

source_name: FFPE-DNA from N04


title: RNA-seq_D1_MDDCs_Pam3CSK4

source_name: Human monocyte-derived dendritic cells

value: Human monocyte-derived dendritic cells

value: Donor 1


title: Adult medulloblastoma sample N08

source_name: FFPE-DNA from N08


title: RNA-seq_D2_mono_unstimulated

value: Donor 2

value: NT


title: Maternal_blood_ASD_48


title: invivo_crispr_ctrl_trim28fl_798

value: Trim28 floxed mice


title: RNA-seq_D2_mono_R837


title: Adult medulloblastoma sample N06

source_name: FFPE-DNA from N06

value: Adult medulloblastoma


title: RNA-seq_D1_MDDCs_R848


title: npc_ko_g13_851

value: In vitro CRISPR

value: KO

value: Rosa26-Cas9 knock-in mice


title: Adult medulloblastoma sample N01

source_name: FFPE-DNA from N01


title: Adult medulloblastoma sample N02

source_name: FFPE-DNA from N02


title: RNA-seq_D1_MDDCs_LPS


title: RNA-seq_D2_mono_Pam3CSK4

value: Human monocytes


title: Maternal_blood_ASD_54

value: F


title: RNA-seq_D1_MDMs_LPS

value: Human monocyte-derived macrophages


title: 421_Wang_input_BWX4207

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -109˚ (XDS)2 (loxP-spec-loxP)

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1 independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al. 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature. Staphylococcus aureus strains were derived from HG003 (Herbert et al. 2010, PMID: 20212089). Cells were grown in tryptic soy broth (TSB) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al., 2013, PMID: 24158908; Wang et al. 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-PrC, or anti-His antibodies according to previous publication (Graham et al. 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina HiSeq2500, Nextseq550, or MiSeq sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

tag: protocol

value: CH, 37degree C

tag: genotype

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)2 (loxP-spec-loxP)

tag: strain

tag: antibody

value: none, input


title: npc_ko_g4_873

tag: guide (if applicable)


title: Batf3 wt cDCs

city: Woolloongabba

first: Chenhao

last: Zhou

state: QLD

address: 37 Kent Street

country: Australia

institute: The University of Queensland Frazer Institute

data_processing:
The Illumina sequencing output was processed using the 10x Genomics Cell Ranger 3´ gene expression and feature barcoding pipeline (v3.0.2). Illumina bcl2fastq (v2.2.0) was used to demultiplex the raw Illumina reads and generate FASTQ files for individual RNA and ADT libraries.
Cellranger count was used to map the sequencing reads to the GRCm38 (mm10) mouse reference genome, and the aggregate function was used to combine the libraries into a single matrix and correct for differences in sequencing depth. The aggregated gene expression and antibody count data, comprising wildtype and knockout libraries were further processed and analysed using Seurat (v3.0.5).
Filtering and quality control were performed to remove outlier cells and transcripts. Every transcript had to be present in at least 3 cells, and a preliminary filtering of cells was done to remove cells with fewer than 200 transcripts. WT and Batf3-/- cells were then separated into two datasets. Further filtering of each dataset was done based on number of transcripts in each cell with a lower threshold of 500 transcripts and the maximum number of transcripts per cell set to 5000. Cells with mitochondrial or ribosomal reads accounting for more than 20% and 50% respectively, were excluded from downstream analysis.
Cell-cell gene expression variation was normalised using log transformation and the antibody counts were normalised using centered log-ratio (CLR), each followed by scaling as implemented in the Seurat pipeline.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: txt.gz (tsv), fastq.gz

molecule: polyA RNA

source_name: conventional dendritic cells

extract_protocol:
Spleens were collected from mice and digested enzymatically and mechanically. Single cell suspensions underwent red blood cell lysis using ammonium chloride potassium (ACK) buffer and T and B cell depletion using EasySep Mouse Streptavidin RapidSpheres (StemCell Technologies). After that, live MHCII+CD11c+ cells were sorted from single cell suspensions via flow cytometric activated cell sorting. Sorted cells were stained with TotalSeq-A antibodies (Biolegend) and then counted for viability and numbers prior to loading into droplets.
Cells were loaded onto the chip for Chromium Single Cell Gel Bead and Library Kit v3 (10x Genomics). The 10x Genomic User Guide was followed for GEM generation and barcoding, cDNA amplification and library construction. Eleven cDNA amplification cycles were performed, and one quarter of the cDNA was used as input for library construction. Library construction for CITE-seq was conducted in accordance to Totalseq-A antibody manufacturer protocol (Biolegend, v.3). Final indexing PCR was performed in a C1000 Touch thermal cycler with a Deep Well Reaction Module (Bio-Rad). For gene expression and CITE-seq libraries 11 and 10 SI-PCR cycles were used, respectively. Using the High Sensitivity DNA kit on Agilent BioAnalyser 2100 the libraries were quantified (Agilent, 5067-4626). Equimolar ratios were used to pool gene expression libraries, and of the total sequencing pool concentration 10% were spiked in cell hashing libraries. Quantification of the final pool was conducted by qPCR using KAPA Library Quantification Kit in combination with the Life Technologies Viia 7 real time PCR instrument (KAPA Biosystems, KK4824). Illumina NextSeq-500 was used for sequencing the denatured libraries using a 150 cycle High-Output Kit. This included Read 1 (28 bp) supplying the cell’s barcode (16nt) and UMI (12nt), i7 (8bp) for sample index and Read 2 (111 bp) to capture the 3’ sequence of the transcripts. In total, two sequencing runs were performed to obtain an average read depth of ~30,000 reads per cell.

value: wildtype

tag: age

value: 8 weeks

value: female

tag: tissue

value: spleen


title: Maternal_blood_ASD_40

value: ASD

value: MARBLES

value: Y


title: RNA-seq_D1_MDMs_Pam3CSK4

value: Donor 1


title: RNA-seq_D1_MDMs_unstimulated

value: NT


title: 420_Wang_input_BWX4205

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -109˚ (XDS)1 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)1 (loxP-spec-loxP)


title: Adult medulloblastoma sample N03

source_name: FFPE-DNA from N03

tag: disease

value: Adult medulloblastoma

tag: gender

value: male


title: npc_ko_g4_848

tag: experiment

value: In vitro CRISPR

tag: condition

value: KO

value: Rosa26-Cas9 knock-in mice


title: npc_ko_g3_870


title: Maternal_blood_ASD_39

tag: diagnosis

tag: Sex

value: M

tag: study

tag: array batch


title: RNA-seq_D1_mono_R837

tag: cell type

value: Human monocytes

tag: donor

tag: treatment


title: Maternal_blood_ASD_43

tag: nutrient metabolites


title: RNA-seq_D1_MDMs_R848

source_name: Human monocyte-derived macrophages

value: Human monocyte-derived macrophages


title: Batf3 ko cDCs

tag: strain

tag: genotype

value: 8 weeks


title: npc_ko_g3_845

tag: guide (if applicable)

tag: genotype/variation


title: Maternal_blood_ASD_41

value: F


title: 417_Wang_input_BWX3910

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -109˚ (XDS)12 (loxP-kan-loxP), xerD(Y277F) (loxP-cat-loxP)

tag: protocol

value: CH, 37degree C

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)12 (loxP-kan-loxP), xerD(Y277F) (loxP-cat-loxP)

tag: antibody

value: none, input


title: Maternal_blood_ASD_42

value: ASD

value: MARBLES

value: Y


title: Maternal_blood_ASD_38

value: N


title: RNA-seq_D1_MDMs_R837

value: Donor 1


title: RNA-seq_D1_mono_LPS


title: RNA-seq_D1_MDDCs_unstimulated

value: Human monocyte-derived dendritic cells

value: NT


title: 414_Wang_input_BWX3872

description: parS∆9 no a.b., -59˚ parS loxP-kan-loxP), -109˚ (XDS)12 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -59degree parS loxP-kan-loxP), -109degree (XDS)12 (loxP-spec-loxP)


title: 419_Wang_input_BWX3974

description: xerC-prC (spec)

value: xerC-prC (spec)


title: RNA-seq_D1_mono_R848


title: 418_Wang_input_BWX3970

description: xerD-prC (spec)

value: xerD-prC (spec)


title: 416_Wang_input_BWX3903

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), ycgO::tetR-cfp (phleo), -109˚ tetO48 (cat)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), ycgO::tetR-cfp (phleo), -109degree tetO48 (cat)


title: RNA-seq_D1_mono_unstimulated

value: Human monocytes


title: 409_Wang_ChIPSMC_BWX4207

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)2 (loxP-spec-loxP)

value: ChIP using anti-SMC antibodies


title: 415_Wang_input_BWX3898

description: xerD (Y277F)-mgfp mut3 (spec)

value: CH, 37degree C

value: xerD (Y277F)-mgfp mut3 (spec)


title: 407_Wang_ChIPSMC_BWX3910

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)12 (loxP-kan-loxP), xerD(Y277F) (loxP-cat-loxP)


title: Veh_2

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.38.
Paired end 100 bp reads generated from the 22RV1 RNA sequencing were mapped using HISAT2 to the Homo sapiens hg19 genome build and raw counts per quantified using HTSeq.
Fragments per kilobase of transcript per million mapped reads (FPKM) for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

growth_protocol: 22RV1 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were purified using RNeasy Plus Mini Kit (Qiagen).
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions.

treatment_protocol: 22RV1 cells were treated with vehicle (DMSO) or 10 nM bruceantin for 24 hr.

value: castration-resistant prostate cancer cells

tag: cell line

tag: agent

value: DMSO


title: BCT_3

value: 10 nM bruceantin


title: 413_Wang_input_BWX3870

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -80˚ (XDS)12 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -80degree (XDS)12 (loxP-spec-loxP)

value: none, input


title: 406_Wang_ChIPSMC_BWX3903


title: Veh_1


title: Maternal_blood_ASD_36

value: ASD

value: M

value: MARBLES

value: N


title: Maternal_blood_ASD_35

value: F

value: Y


title: Maternal_blood_ASD_34


title: Maternal_blood_ASD_33


title: Maternal_blood_ASD_37


title: Maternal_blood_ASD_31


title: 3V8

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description:
Vegetative 8 hours
Experiment 2

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: dicty_2.7
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts, or individual raw count files for each sample produced the same way

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum

growth_protocol: Dictyostelium discoideum (D. discoideum) strain Ax4 was purchased from the Dictybase stock center. Vegetatively growing cells were axenically maintained in shaking culture in HL5 nutrient medium (14.3 g/L bacto peptone, 7.15 g/L yeast extract, 18 g/L maltose monohydrate, 0.641 g/L Na2HPO4, 0.49 g/L KH2PO4, supplemented with biotin, cyanocobalamin, folic acid, lipoic acid, riboflavin and thiamine-HCl). Starvation and consequent aggregation were induced by washing D. discoideum four times in development buffer (DB; 5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, 2 mM MgCl2 in autoclaved H2O) and plating at a density of 2 x 106 cells/ml in DB on tissue culture-treated plates, without shaking. As a control, vegetatively growing cells were plated at a density of 2 x 106 cells/ml in HL5 on tissue culture-treated plates, without shaking.

extract_protocol:
Total RNA was isolated using the RNEasy kit (Qiagen) and quantified using the Qubit 2.0 (ThermoFisher).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: In one experiment, cells were starve for 30 minutes, 4 or 8 hours. In another experiment cells were starved for 30 minutes or 8 hours with or without added reduced glutathione. Time and supplement matched vegetative controls were included.

value: Vegetative 8 hours


title: Maternal_blood_ASD_28


title: Maternal_blood_ASD_32


title: Maternal_blood_ASD_29


title: Maternal_blood_ASD_26


title: 404_Wang_ChIPSMC_BWX3870


title: Maternal_blood_ASD_30


title: 410_Wang_input_BWX3270_rep4

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.)


title: BCT_2


title: 3V0-5

description:
Vegetative 30 minutes
Experiment 2

value: Vegetative 30 minutes


title: BCT_1


title: 403_Wang_ChIPSMC_BWX3381_rep2

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP)

value: CH, 37degree C

value: parS<delta>9 no a.b., -117degree parS (loxP-kan-loxP)

value: ChIP using anti-SMC antibodies


title: RNA-seq_D1_mono_Pam3CSK4

source_name: Human monocytes

value: Human monocytes

value: Donor 1


title: Maternal_blood_ASD_25


title: Veh_3

value: castration-resistant prostate cancer cells

value: DMSO


title: 408_Wang_ChIPSMC_BWX4205

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)1 (loxP-spec-loxP)


title: 401_Wang_ChIPPrC_BWX3974

description: xerC-prC (spec)

value: xerC-prC (spec)

value: ChIP using anti-PrC antibodies


title: 405_Wang_ChIPSMC_BWX3872

value: parS<delta>9 no a.b., -59degree parS loxP-kan-loxP), -109degree (XDS)12 (loxP-spec-loxP)


title: 3D0-5

description:
Starved 30 minutes
Experiment 2

value: Starved 30 minutes


title: wt_GSP

city: Boston

first: Richard

middle: I

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

data_processing:
Raw data was processed using 10X’s cellranger (version 1.3.1). Illumina BCL files were demultipled using `cellranger mkfastq`. Then, `cellranger count` was used to generate single-cell gene counts.
Transcriptomic reads were mapped to the mm10 reference genome. For the GFP/Che transcriptomic dataset, the reference was augmented with the expected Tdgf1 transcript. Gene-specific reads were mapped to the 3 genes targeted for gene-specific enrichment: Msh2, Tdgf1 and Zfp42. gRNA were mapped to the known set of gRNA sequences.
UMI-unique counts for each gRNA were modeled as a two-component mixture model, with one component corresponding to counts arising from noise, and another component corresponding to counts arising from the presence of the gRNA in the cell. Models were initialized using the clustering results of a Gaussian mixture model, and then fit using expectation-maximization. A gRNA was defined to be present in a cell if the probability of the counts arising from the noise component was less than 0.05.
For analysis of differential expression of target genes and for visualization, counts were first normalized using estimated size factors and then log transformed after adding a pseudocount of 1. The Wilcoxon test was then applied on log-normalized counts.
Cells containing a single gRNA and that had a high quality transcriptome were retained for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Gene-barcode matrices are stored as matrices in *mtx files, with gene and barcode metadata in *tsv files. These are generated by 10X, and more information on the format can be found here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/1.3/output/matrices. Filtered gene-barcode matrices are provided for transcriptomic and gene-specific samples, while raw gene-barcode matrices are provided for gRNA samples.
Supplementary_files_format_and_content: gRNA assignments for each cell are stored in *csv files.

growth_protocol: Mouse embryonic stem cells were cultured in Knockout DMEM (Thermo Fisher) with 15% defined fetal bovine serum (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), Glutamax (Thermo Fisher), 0.55 mM 2-mercaptoethanol (Sigma), ESGRO LIF (Millipore), 5 nM GSK-3 inhibitor XV (Sigma) and 500 nM UO126 (Sigma).

extract_protocol:
For each dataset, cell lines were mixed at equal concentrations and the resulting pool was prepared for 10X Chromium scRNA-seq 48h later. Cells were single-cell dissociated with Accutase (Sigma-Aldrich), centrifuged and resuspended in 1mL pre-chilled DPBS+0.04%BSA. Cells were counted and resuspended in DPBS+0.04%BSA following the 10xChromium Volume Calculator Table for a total of 10,000 targeted cells
Preparation of 10X Chromium scRNA-seq transcriptome libraries for sequencing was carried out largely using the standard protocol. In order to maintain gRNAs in the library, which are shorter than standard transcripts, SPRI purification was altered as follows: purification of cDNA was carried out with 1.6X beads instead of the standard 0.8X, post-fragmentation purification was performed with 1.6X instead of 0.8X, post-adapter ligation purification was performed with 1.4X instead of 0.8X, and post-SI PCR was performed with 1.2X instead of 0.8X. Additionally, to reserve a portion of cDNA and allow for custom applications such as gRNA sequence capture, two additional PCR cycles (12 instead of 10) were performed at the cDNA amplification stage. Half of the product was used for the transcriptome prep, ¼ was amplified to obtain the required amount for gRNA sequence capture, and 1/8 was used for gene-specific PCR enrichment.

treatment_protocol: CRISPR/Cas9 reagents were added by Lipofectamine 3000 transfection along with Tol2 transposase and stable drug selection for cells receiving Cas9 (Blasticidin resistant) and gRNA (Hygromycin resistant).

tag: strain background

value: Mouse embryonic stem cells

value: Wild type

tag: enrichment

value: Gene-specific enrichment


title: wt_txm


title: 3V4

description:
Vegetative 4 hours
Experiment 2

value: Vegetative 4 hours


title: Maternal_blood_ASD_27

tag: diagnosis

value: ASD

tag: Sex

value: M

value: MARBLES

value: Y


title: 281_Wang_input_BWX3834_1mMIPTG_60min

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), yrvN (-122˚):: tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1)  independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature. Staphylococcus aureus strains were derived from HG003 (Herbert et al 2010, PMID: 20212089). Cells were grown in tryptic soy broth (TSB) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, or anti-His antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina HiSeq2500, Nextseq550, or MiSeq sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 1mM IPTG for 60 min

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), yrvN (-122degree)::tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm

value: none, input


title: Maternal_blood_ASD_20

tag: study

tag: array batch


title: GFPChe_GSP

source_name: mESCs_GFP/mCherry -/-

tag: cell type

value: GFP/mCherry -/-


title: 280_Wang_input_BWX3908

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-kan-loxP), ∆xerD (loxP-erm-loxP)

value: CH, 37degree C

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerD (loxP-erm-loxP)


title: 2V4

description:
Vegetative 4 hours
Experiment 2

tag: treatment


title: 2V8

description:
Vegetative 8 hours
Experiment 2

value: Vegetative 8 hours


title: Beas-2B_30WSP-2_PRO-seq

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

data_processing:
Library strategy: PRO-seq
Reads were trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘literal=AAAAAAAAAAAAAAAAAAAAAAA ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25’.
Trimmed reads were mapped to the human genome (hg38) using hisat2 (v. 2.1.0) and hg38 indexes downloaded from UCSC with settings '--very-sensitive and --no-spliced-alignment'.
Resulting SAM files were converted to BAM format using samtools view (v. 1.8) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.25.0) for both positive and negative strands with arguments ‘-bg -ibam -g hg38 -strand [+/-]’. The fourth column (read coverage) of the negative strand file was negated and then concatenated with the positive strand file to generate a strand-differentiated bedGraph file.
FStitch (v. 1.0) was first used to filter regions of inactive transcription in all samples to lessen downstream compute processing requirements. FStitch train was used with arguments ‘-r (sample.positiveStand.bedGraph) -t (trainingFile.bed) -o (outputTrainingParameters.hmminfo)’ using the IGV (v. 2.3.75) Region Navigator tool to produce a BED format training file generated from one of the 10 min dex-treated samples that was determined to be most representative of the data in terms of read coverage, complexity, and total reads mapped.
FStitch segment was then run on all single-strand non-normalized bedGraph files with arguments ‘-r (sample.pos.bedgraph) -w (outputTrainingParameters.hmminfo) -o (sample.bed)’. Positive and negative strand files were then concatenated and sorted using sortBed in the BEDTools suite (v. 2.25.0).
Tfit (v. 1.0) was used to generate the predictions of bidirectionals/eRNAs. BED file annotations of preliminary bidirectional calls were generated using the Tfit bidir old module with arguments ‘-ij (sample.concatenated.bedGraph) -N (bidir old) -k (sample.concatenatedFStitch.bed) -mle 1 -o (output directory) -log out (output directory) -tss (hg38 RefSeq gene transcription start site file).
Using the bidirectional predictions file, the Tfit model module was run to get higher confidence calls with arguments ‘-ij (sample.concatenated.bedGraph) -k (preliminaryBidirectionals.bed) -N (tfit mod) -log out (output directory) -o (output directory) -config (config file)’ to produce a final BED annotation file of predicted bidirectionals.
Using the RefSeq : NCBI Reference Sequences for hg38, including both NM and NR accession types (downloaded from the UCSC track browser on May 18, 2018), counts were calculated for each sorted BAM file using multibBamCov in the BEDTools suite (v. 2.25.0). Genes (NM accession type) and lncRNAs (NR accession type) were then filtered such that only the isoform with the highest number of reads per annotated length was kept in order to minimize duplicate samples being included in differential transcription analysis.
DESeq2 (v. 1.20.0, Bioconductor release v. 3.7) was then used to determine which genes were differentially transcribed between the different cell types. For bidirectional/enhancer comparisons, all bidirectional prediction Tfit calls were first merged using mergeBed (argument -d 60) from the BEDTools suite (v. 2.25.0) to generate an annotation file. Counts were then calculated for each sample using multicov from the BEDTools suite (v. 2.25.0) and DESeq2 was used to calculate differentially transcribed bidirectionals/eRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files are non-normalized, strand-differentiated coverage files, as described above.

source_name: BEAS-2B airway epithelial cells

growth_protocol: Beas-2B immortalized human bronchial epithelial cells were obtained from ATCC and cultured in Dulbecco’s Modified Eagle Medium (DMEM; Corning) with L-glutamine and 4.5 g/L glucose supplemented with 10% Fetal Bovine Serum (FBS; VWR) and 1% penicillin/streptomycin (Corning)

extract_protocol:
Plates were washed in PBS and cells were scraped in Lysis Buffer prior to isolation of nuclei. Nuclear run-on reactions were performed on aliquots of 10 million nuclei in the presence of Biotin-11-CTP, then total RNA was isolated using TRIzol LS Reagent (Invitrogen). RNA was hydrolyzed with NaOH to yield fragments ~100 bp long and nascent RNA was enriched using M-280 Streptavidin Dynabeads (Invitrogen).
Sequencing adapters were ligated onto 3' ends of nascent RNA and then a second enrichment was performed using streptavidin beads. 5' ends were de-capped (RppH) and repaired (PNK) prior to ligation of sequencing adapters and the third and final streptavidin bead enrichment. Reverse transcription was then performed and purified cDNA libraries were amplified for sequencing in PCR reactions containing Illumina TruSeq Small RNA PCR Index Primers to differentially barcode the libraries and enable multiplexing. PCR-amplified libraries were size-selected for a range of ~140–350 bp (average fragment length ~250 bp) using Agencourt AMPure XP beads (Beckman Coulter) at a volume of 1X as instructed by the manufacturer. Libraries were then pooled and sequenced on an Illumina NextSeq instrument using 75 bp single-end reads.

treatment_protocol: For PRO-seq, BEAS-2B cells were plated on 3 x 15 cm tissue culture dishes and grown to confluence. Cells were harvested after exposure to WSP for 30 and 120 min.

value: airway epithelial cells

tag: molecule subtype

value: nascent RNA


title: Maternal_blood_ASD_24

tag: nutrient metabolites


title: GFPChe_txm

value: Mouse embryonic stem cells


title: 402_Wang_ChIPSMC_BWX3270_rep4

tag: genotype

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.)

tag: strain

value: ChIP using anti-SMC antibodies


title: Beas-2B_120WSP-1_PRO-seq


title: 3D8

description:
Starved 8 hours
Experiment 2

value: Starved 8 hours


title: Beas-2B_120WSP-2_PRO-seq


title: Beas-2B_veh-2_PRO-seq


title: 2V0-5

description:
Vegetative 30 minutes
Experiment 2

value: Vegetative 30 minutes


title: 3D4

description:
Starved 4 hours
Experiment 2

value: Starved 4 hours


title: Maternal_blood_ASD_23

value: ASD

value: M

value: MARBLES


title: 277_Wang_input_BWX3799

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 4x XDS (loxP-spec-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 4x XDS (loxP-spec-loxP)


title: Beas-2B_30WSP-1_PRO-seq


title: 2D4

description:
Starved 4 hours
Experiment 2


title: Beas-2B_veh-1_PRO-seq


title: 278_Wang_input_BWX3821

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-spec-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-spec-loxP)

value: none, input


title: 2D8

description:
Starved 8 hours
Experiment 2


title: Maternal_blood_ASD_22

description: nutrient metabolites: Y: yes, we have metabolites data for that sample; N: no, we don't have metabolites data for that sample.  Nutrient metabolites information is included in the paper supplementary tables. There are multiple metabolites and different samples have different metabolites, as detailed in the paper methods and supplementary tables.

value: Y


title: Beas-2B_120WSP-2_ATAC-seq

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.29.2) with arguments ‘-bg -ibam -g hg38 -strand +’.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files are non-normalized coverage files.

extract_protocol:
Cells were washed twice with 1X PBS and collected by scraping or pelleting prior to counting. Approximately 50K cells were pelleted and processed in duplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 37 bp paired-end reads.

treatment_protocol: Wood Smoke Particles (WSP) were generated as described (14) and generously gifted by Dr. Andrew Ghio at the Environmental Protection Agency Laboratory in North Carolina. Particles were dehydrated for transportation and resuspended in PBS. Particles were disaggregated by sonication and sterilized under UV light for 20 minutes prior to addition directly to cell culture media at a concentration of 1 mg/ml for all experiments.


title: Maternal_blood_ASD_21

value: F


title: Maternal_blood_ASD_17


title: 273_Wang_input_BWX3732

description: xerD-mgfp mut3 (spec), yrdQ-XDS1 (loxP-kan-loxP)

value: CH, 37degree C


title: Maternal_blood_ASD_19


title: Maternal_blood_ASD_18


title: Beas-2B_120WSP-1_ATAC-seq

value: airway epithelial cells


title: 2D0-5

description:
Starved 30 minutes
Experiment 2

value: Starved 30 minutes


title: 279_Wang_input_BWX3906

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-kan-loxP), ∆xerC (loxP-erm-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerC (loxP-erm-loxP)


title: 272_Wang_input_BWX3721

description: xerD-mgfp mut3 (spec), ∆XDS1 (1717kb) (loxP-kan-loxP)

value: xerD-mgfp mut3 (spec), deltaXDS1 (1717kb) (loxP-kan-loxP)


title: Beas-2B_30WSP-1_ATAC-seq


title: 276_Wang_input_BKM680

description: rtp-yfp (spec)

value: rtp-yfp (spec)


title: Beas-2B_30WSP-2_ATAC-seq


title: 271_Wang_input_BWX3677

description: xerD-mgfp mut3 (spec), ∆xerC (loxP-erm-loxP)

value: xerD-mgfp mut3 (spec), deltaxerC (loxP-erm-loxP)


title: 1V8

description:
Vegetative 8 hours
Experiment 2

value: Vegetative 8 hours


title: 1V4

description:
Vegetative 4 hours
Experiment 2

value: Vegetative 4 hours


title: Beas-2B_veh-2_ATAC-seq


title: 270_Wang_input_BWX3658

description: xerD-mgfp mut3 (spec), ∆dif (loxP-kan-loxP)

value: xerD-mgfp mut3 (spec), deltadif (loxP-kan-loxP)


title: Beas-2B_veh-1_ATAC-seq


title: Huh 48h IP 3

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description:
human_counts.txt
H2_ip_3

data_processing:
Adapters were trimmed using fastp.
Trimmed reads were first aligned to a file of known repetitive sequences. These reads were discarded.
Remaining reads were then aligned to the SARS-CoV-2 genome
Remaining reads were then aligned to the host genome (human or monkey)
Counts were quantified using featureCounts
Genome_build: hg38 or ChlSab1.1
Supplementary_files_format_and_content: filtered counts matrix

source_name: Huh7.5 cells

growth_protocol: Cell lines were cultured using standard media and passaging conditions.

extract_protocol:
Sample proteins were digested and RNA was extracted via commercial spin column (Zymo).
TAKARA Bio SMART-Seq library prep kit was used to prepare RNA-seq libraries
Paired end RNA sequencing

treatment_protocol: Cells were either not infected with SARS-CoV-2, or infected for 24 or 48 hours. In each of these conditions, bulk RNA seq was performed (input) and also RNA-seq after crosslinking and pulldown for the SARS-CoV-2 viral RNA.

tag: infection duration

value: SARS-CoV-2 infection, 48h

tag: pulldown

value: Yes


title: Huh 48h Input 3

description:
human_counts.txt
H2_in_3

value: No


title: 268_Wang_input_BWX3676

description: xerC-mgfp mut3 (spec), ∆xerD (loxP-erm-loxP)

tag: protocol

value: xerC-mgfp mut3 (spec), deltaxerD (loxP-erm-loxP)

tag: antibody


title: 267_Wang_input_BWX3657

description: xerC-mgfp mut3 (spec), ∆dif (loxP-kan-loxP)

value: xerC-mgfp mut3 (spec), deltadif (loxP-kan-loxP)

value: none, input


title: Maternal_blood_ASD_14

value: ASD

value: M

value: MARBLES

value: Y


title: Huh 48h IP 2

description:
human_counts.txt
H2_ip_2

tag: cell line


title: 1D4

description:
Starved 4 hours
Experiment 2

value: Starved 4 hours


title: Huh 48h Input 2

description:
human_counts.txt
H2_in_2


title: 266_Wang_input_BWX3653

description: xerC-mgfp mut3 (spec)

value: CH, 37degree C

value: xerC-mgfp mut3 (spec)


title: Maternal_blood_ASD_16


title: Dicty_8vg_3

description:
Vegetative 8 hours plus GSH
Experiment 1

value: Vegetative 8 hours plus GSH


title: Maternal_blood_ASD_15


title: Maternal_blood_ASD_12


title: Huh 48h IP 1

description:
human_counts.txt
H2_ip_1


title: Maternal_blood_ASD_9


title: Dicty_8vg_2


title: Maternal_blood_ASD_13


title: Maternal_blood_ASD_10

value: F


title: 1V0-5

description:
Vegetative 30 minutes
Experiment 2

value: Vegetative 30 minutes


title: Maternal_blood_ASD_11


title: Dicty_8vg_1


title: Maternal_blood_ASD_7


title: 264_Wang_input_BWX3453

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆xerC (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaxerC (loxP-erm-loxP)


title: Maternal_blood_ASD_6


title: 265_Wang_input_BWX3474

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆xerD (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaxerD (loxP-erm-loxP)


title: 269_Wang_input_BWX3655

description: xerD-mgfp mut3 (spec)

value: xerD-mgfp mut3 (spec)


title: Huh 48h Input 1

description:
human_counts.txt
H2_in_1

value: SARS-CoV-2 infection, 48h

value: No


title: Dicty_8v_3

description:
Vegetative 8 hours control
Experiment 1

value: Vegetative 8 hours control


title: Huh 24h IP 3

description:
human_counts.txt
H1_ip_3

value: SARS-CoV-2 infection, 24h

value: Yes


title: Maternal_blood_ASD_8

value: ASD

value: M


title: 262_Wang_input_BWX3463

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆spoIIIE (loxP no. a.b.), ∆sftA (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaspoIIIE (loxP no. a.b.), deltasftA (loxP-erm-loxP)

value: none, input


title: Dicty_8v_1

description:
Vegetative 8 hours control
Experiment 1


title: Maternal_blood_ASD_5

value: MARBLES

value: Y


title: Huh 24h Input 3

description:
human_counts.txt
H1_in_3


title: Huh 24h IP 2

description:
human_counts.txt
H1_ip_2


title: Maternal_blood_ASD_4

value: N


title: 258_Wang_ChIPSMC_BWX3908

value: CH, 37degree C

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerD (loxP-erm-loxP)

value: ChIP using anti-SMC antibodies


title: 261_Wang_input_BWX3452

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆rtp (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltartp (loxP-erm-loxP)


title: Huh 24h Input 2

description:
human_counts.txt
H1_in_2


title: Dicty_8dg_3

description:
Starved 8 hours plus GSH
Experiment 1

value: Starved 8 hours plus GSH


title: Dicty_8dg_1

description:
Starved 8 hours plus GSH
Experiment 1


title: Dicty_8dg_2

description:
Starved 8 hours plus GSH
Experiment 1


title: Huh 24h IP 1

description:
human_counts.txt
H1_ip_1


title: 263_Wang_input_BWX3526

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆dif (loxP-spec-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltadif (loxP-spec-loxP)


title: inter respiratory burst rep1

city: Utrecht

first: Robert-Jan

last: Bleichrodt

address: Padualaan 8

country: Netherlands

institute: Utrecht University

data_processing:
Single-end sequence reads were generated using the Illumina HiSeq2500 system. FASTQ sequence files were generated using bcl2fastq2 version 2.18. Initial quality assessment was based on data passing the Illumina Chastity filtering. Subsequently, reads clipped (up to minimum read length of 50bp. The second quality assessment was based on thecontaining PhiX control signal were removed using an in-house filtering protocol. In addition, reads containing (partial) adapters were remaining reads using the FASTQC quality control tool version 0.11.5. The final quality scores per sample are provided as Enclosure.
HISAT version 2.1.0 (Kim, Langmead, & Salzberg, 2015) was used to align sequence reads to the Agabi_varbisH97_2 version of the A. bisporus H97 genome (E Morin et al., 2012), which was obtained from MycoCosm (Grigoriev et al., 2014).
Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al., 2010), was used to identify reads mapping to predicted genes and to identify differentially expressed genes. The bias correction method was used while running Cuffdiff (Roberts, Trapnell, Donaghey, Rinn, & Pachter, 2011). Cuffdiff normalizes the expression level of each predicted gene to fragments per kilobase of exon model per million fragments (FPKM).
Genome_build: Agabi_varbisH97_2 version of the A. bisporus H97 genome
Supplementary_files_format_and_content: Cuffdiff output (gene_exp.diff)

organism: Agaricus bisporus

source_name: Phase III compost mycelium

growth_protocol: A. bisporus strain A15 rye spawn (8 g) was inoculated in phase II compost (1 kg) (CNC, Milsbeek, the Netherlands) at 25 °C until temperature peaks developed (as measured with a DS18B20 sensor which was placed in the compost). Boxes were overlayed with plastic film with small holes to allow for a high humidity.

extract_protocol:
Samples were crushed in LN using mortar and pestle and further ground to a fine powder for 1 min using a Tissuelyser II with a LN pre-cooled steel grinding jar (Qiagen, Venlo, Netherlands) at 30 Hz.
Strand-specific mRNA-seq libraries for the Illumina platform were generated and sequenced at BaseClear BV (Leiden, The Netherlands). High-quality total RNA (checked and quantified on a Bioanalyzer (Agilent)) was used as input for the so-called dUTP library preparation method (Parkhomchuk D et al, Nucleic Acid Research 2009; Levin J et al, Nature Methods 2010). Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random hexamers in the presence of Actinomycin D. The second-strand synthesis was perform incorporating dUTP instead of dTTP. Barcoded DNA adapters were ligated to both ends of the double-stranded cDNA and subjected to a PCR amplification. The resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2500 (HiSeq Rapid SBS v2 chemistry) with a single-read 50 cycles sequencing protocol and indexing.

treatment_protocol: ~7.5 g compost samples from the immediate surrounding of temperature sensors were harvested, wrapped in aluminium foil, immediately frozen in liquid nitrogen (LN), and stored at -80 °C.

tag: time

value: ~8.5 h after a burst started


title: inter respiratory burst rep3


title: inter respiratory burst rep2


title: 257_Wang_ChIPSMC_BWX3906

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerC (loxP-erm-loxP)


title: Dicty_8v_2

description:
Vegetative 8 hours control
Experiment 1

value: Vegetative 8 hours control


title: Maternal_blood_ASD_2


title: Dicty_8d_3

description:
Starved 8 hours control
Experiment 1

value: Starved 8 hours control


title: after respiratory burst rep3

value: ~4.5 h after a burst started


title: Huh Mock Input 3

description:
human_counts.txt
HM_in_3

value: No


title: 256_Wang_ChIPSMC_BWX3821

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-spec-loxP)


title: 255_Wang_ChIPSMC_BWX3799

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 4x XDS (loxP-spec-loxP)


title: 259_Wang_ChIPSMC_BWX3834_1mMIPTG_60min

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), yrvN (-122˚):: tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm

value: CH, 37degree C, 1mM IPTG for 60 min

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), yrvN (-122degree)::tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm


title: Maternal_blood_ASD_1

value: ASD

value: M

value: MARBLES

value: Y


title: Dicty_8d_2

description:
Starved 8 hours control
Experiment 1


title: Huh Mock IP 2

description:
human_counts.txt
HM_ip_2

value: Yes


title: Dicty_8d_1

description:
Starved 8 hours control
Experiment 1


title: after respiratory burst rep2


title: after respiratory burst rep1


title: Huh Mock Input 2

description:
human_counts.txt
HM_in_2


title: Dicty_30vg_3

description:
Vegetative 30 minutes plus GSH
Experiment 1

value: Vegetative 30 minutes plus GSH


title: Huh 24h Input 1

description:
human_counts.txt
H1_in_1

value: SARS-CoV-2 infection, 24h


title: Maternal_blood_ASD_3


title: Huh Mock IP 1

description:
human_counts.txt
HM_ip_1


title: respiratory burst rep3

value: ~0.5 h after a burst started


title: Dicty_30vg_2


title: 250_Wang_ChIPGFP_BWX3721

value: CH, 37degree C

value: xerD-mgfp mut3 (spec), deltaXDS1 (1717kb) (loxP-kan-loxP)

value: ChIP using anti-GFP antibodies


title: Huh Mock Input 1

description:
human_counts.txt
HM_in_1


title: respiratory burst rep2


title: Dicty_30vg_1


title: A549 FOXM1 PREX 2

first: David

last: Kozono

address: 450 Brookline Avenue

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description:
20190416_12-sgFOXM1-2_plusPrex_12_AS6801_S11
FOXM1 knockout A549 cells treated with 100 nM prexasertib, replicate 2

data_processing:
Reads were mapped to Hg19 using STAR alignment
Counts were generated using HTseq
Genome_build: Hg19
Supplementary_files_format_and_content: text files with counts for every gene

source_name: A549_FOXM1 sgRNA knockout_100 nM prexasertib

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% pen/strep, at 37ºC in 5% CO2

extract_protocol:
Qiagen RNeasy Plus
Kappa stranded mRNA Hyper Prep

treatment_protocol: Cells were synchronized into S phase, released for 1 hour, and treated with 100 nM prexaertib or DMSO (vehicle) for 2 hours

value: lung cancer cell line

value: FOXM1 sgRNA knockout

value: 100 nM prexasertib


title: 248_Wang_ChIPGFP_BWX3658

value: xerD-mgfp mut3 (spec), deltadif (loxP-kan-loxP)


title: Dicty_30v_3

description:
Vegetative 30 minutes control
Experiment 1

value: Vegetative 30 minutes control


title: Dicty_30v_2


title: respiratory burst rep1


title: A549 FOXM1 PREX 1

description:
20190416_11-sgFOXM1-2_plusPrex_11_AS6801_S10
FOXM1 knockout A549 cells treated with 100 nM prexasertib, replicate 1


title: 254_Wang_ChIPGFP_BKM680

description: rtp-yfp (spec)

value: rtp-yfp (spec)


title: SPINDOC KO-2

city: Smithville

first: Bin

last: Liu

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Tophat2 and bowtie2 mapping
DESeq2 for differentially expression anlysis
Genome_build: GRCh38
Supplementary_files_format_and_content: text file

extract_protocol:
Total RNA was isolated from confluent 10cm-dish of HEK293T WT and KO cell lines using a Qiagen RNeasy® Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SPINDOC-/-


title: 247_Wang_ChIPGFP_BWX3655

description: xerD-mgfp mut3 (spec)

value: xerD-mgfp mut3 (spec)


title: A549 FOXM1 DMSO 2

description:
20190416_10-sgFOXM1-2_-DMSO_10_AS6801_S9
FOXM1 knockout A549 cells treated with DMSO vehicle, replicate 2

source_name: A549_FOXM1 sgRNA knockout_DMSO

value: DMSO (vehicle)


title: 246_Wang_ChIPGFP_BWX3676

value: xerC-mgfp mut3 (spec), deltaxerD (loxP-erm-loxP)


title: SPINDOC WT-2

value: Wild type


title: SPINDOC KO-1


title: 245_Wang_ChIPGFP_BWX3657

value: xerC-mgfp mut3 (spec), deltadif (loxP-kan-loxP)


title: A549 FOXM1 DMSO 1

description:
20190416_9-sgFOXM1-2_-DMSO_9_AS6801_S8
FOXM1 knockout A549 cells treated with DMSO vehicle, replicate 1


title: 251_Wang_ChIPGFP_BWX3732

description: xerD-mgfp mut3 (spec), yrdQ-XDS1 (loxP-kan-loxP)


title: Dicty_30v_1


title: Dorsal root ganglion cells-SNI 14d_rep2

city: Shanghai

first: Kaikai

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

description:
raw_UMI_counts_3.txt
raw_UMI_counts_3_metadata.txt

data_processing:
Basecalls were performed using bcl2fastq2-v2.19.1.403
Sequenced reads of 10x genomics were processed using Cell Ranger (version.2.1.0) with default parameters
Sequenced reads of Smart-seq2 were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit (version 0.0.13), then mapped to mm10 using hisat2 (version: 2.0.4), finally,  the reads counts were normalized to FPKM (Fragments Per Kilobase of exon per Megabase of library size)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each single cell
Supplementary_files_format_and_content: tab-delimited text files include raw UNI counts for each single cell
Supplementary_files_format_and_content: tab-delimited text files include cell information

source_name: Dorsal root ganglion cells

extract_protocol:
For Smart-seq2, Total RNA was extracted with AMBION AM1560 kit; for 10x Genomics, The cellular suspensions were further processed with Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v2, 16 rxns PN-120237
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SNI 14d

tag: tissue

value: Dorsal root ganglion

tag: technology

value: 10x genomics


title: 249_Wang_ChIPGFP_BWX3677

description: xerD-mgfp mut3 (spec), ∆xerC (loxP-erm-loxP)

value: CH, 37degree C

value: xerD-mgfp mut3 (spec), deltaxerC (loxP-erm-loxP)


title: Dicty_30dg_2

description:
Starved 30 minutes plus GSH
Experiment 1

value: Starved 30 minutes plus GSH


title: A549 LIN54 DMSO 2

description:
20190416_6-sgLIN54-2_-DMSO_6_AS6801_S5
LIN54 knockout A549 cells treated with DMSO vehicle, replicate 2

source_name: A549_LIN54 sgRNA knockout_DMSO

value: lung cancer cell line

value: LIN54 sgRNA knockout


title: 244_Wang_ChIPGFP_BWX3653

description: xerC-mgfp mut3 (spec)

value: xerC-mgfp mut3 (spec)

value: ChIP using anti-GFP antibodies


title: A549 LIN54 PREX 2

description:
20190416_8-sgLIN54-2_plusPrex_8_AS6801_S7
LIN54 knockout A549 cells treated with 100 nM prexasertib, replicate 2

source_name: A549_LIN54 sgRNA knockout_100 nM prexasertib

value: 100 nM prexasertib


title: A549 LIN54 PREX 1

description:
20190416_7-sgLIN54-2_plusPrex_7_AS6801_S6
LIN54 knockout A549 cells treated with 100 nM prexasertib, replicate 1


title: Dorsal root ganglion cells-SNI 7d_rep2

value: SNI 7d


title: A549 LIN54 DMSO 1

description:
20190416_5-sgLIN54-2_-DMSO_5_AS6801_S4
LIN54 knockout A549 cells treated with DMSO vehicle, replicate 1


title: SPINDOC WT-1


title: 242_Wang_ChIPSMC_BWX3453

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆xerC (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaxerC (loxP-erm-loxP)

value: ChIP using anti-SMC antibodies


title: Dorsal root ganglion cells-SNI 2d_rep2

value: SNI 2d


title: Dicty_30d_2

description:
Starved 30 minutes control
Experiment 1

value: Starved 30 minutes control


title: 243_Wang_ChIPSMC_BWX3474

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆xerD (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaxerD (loxP-erm-loxP)


title: 241_Wang_ChIPSMC_BWX3526

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆dif (loxP-spec-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltadif (loxP-spec-loxP)


title: Dicty_30d_3

description:
Starved 30 minutes control
Experiment 1


title: A549 EV PREX 2

description:
20190416_4-sgEV_plusPrex_4_AS6801_S3
Control (empty vector) A549 cells treated with 100 nM prexasertib, replicate 2

source_name: A549_Wild type_100 nM prexasertib

value: Wild type


title: Dicty_30dg_1


title: 239_Wang_ChIPSMC_BWX3452

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆rtp (loxP-erm-loxP)

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltartp (loxP-erm-loxP)


title: A549 EV DMSO 2

description:
20190416_2-sgEV_-DMSO_2_AS6801_S1
Control (empty vector) A549 cells treated with DMSO vehicle, replicate 2

source_name: A549_Wild type_DMSO

value: DMSO (vehicle)


title: Veg_30

description: 30 control

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 2.2 (10X genomics)
Samples were processed and analyzed in R (3.6.0) using Seurat (v3)
Genome_build: dicty_2.7
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.

extract_protocol:
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller.
Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. An estimated 10,000 cells were added to each channel with an average of 7,000 cells recovered.  Libraries were sequenced on a NovaSeq (Illumina)

treatment_protocol: Cells were starve for 30 minutes or 10 hours. Time matched vegetative controls were included.

value: Starvation 30 minutes


title: KO_MI6: heart ACKR4_KO mice replicate 3

city: Wuhan

first: Min

last: Zhang

state: Hubei

address: 1277 Jiefang Avenue, Wuhan 430022, China

department: Department of Cardiology

institute: Union Hospital, Tongji Medical College of Huazhong University of Science and Technology

description: ACKR4_KO mice replicate 3

data_processing:
The primary sequencing output (FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools.
Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis).
Reads were then mapped to mm10 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).Reads were counted with HTSeq v0.6.0 using the settings union and stranded=no.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

source_name: heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

value: 8-10 weeks


title: Dorsal root ganglion cells-SNI 24h_rep3

value: SNI 24h

value: Dorsal root ganglion

value: 10x genomics


title: Dorsal root ganglion cells-SNI 6h_rep3

value: SNI 6h


title: 240_Wang_ChIPSMC_BWX3463

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆spoIIIE (loxP no. a.b.), ∆sftA (loxP-erm-loxP)

source_name: Bacillus subtilis PY79

value: CH, 37degree C

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP), deltaspoIIIE (loxP no. a.b.), deltasftA (loxP-erm-loxP)


title: Dicty_30d_1

description:
Starved 30 minutes control
Experiment 1


title: Dicty_30dg_3

value: Starved 30 minutes plus GSH


title: A549 EV PREX 1

description:
20190416_3-sgEV_plusPrex_3_AS6801_S2
Control (empty vector) A549 cells treated with 100 nM prexasertib, replicate 1

value: lung cancer cell line

value: 100 nM prexasertib


title: A549 EV DMSO 1

description:
20190416_1-sgEV_-DMSO_AS6801_S13
Control (empty vector) A549 cells treated with DMSO vehicle, replicate 1


title: Veg_10

description: 10 hour control

value: Starvation 10 hours


title: 4b_shMAP3K7_shCHD1_viral_replicate 2

city: Winston-Salem

first: Douglas

middle: Scott

last: Lyles

state: NC

address: Medical Center Blvd.

department: Biochemistry

institute: Wake Forest School of Medicine

data_processing:
base-calling by Illumina Real Time Analysis RTA 2.0
alignment of reads by STAR sequence aligner v2.4.0
counts extracted by FeatureCounts v1.6.1
Genome_build: hg19 and NCBI Reference Sequence: NC_001560.1 for vesicular stomatitis virus
Supplementary_files_format_and_content: tab-delimited text file of raw counts for all samples

growth_protocol: PC3 cells were cultured in RPMI medium with 10% fetal calf serum

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) from three independent samples of each cell line.
Total RNA was used to prepare cDNA libraries using the Illumina® TruSeq Stranded Total RNA with Ribo-Zero Gold Preparation kit (Illumina Inc.)

treatment_protocol: ShControl, shMAP3K7, shCHD1, and shMAP3K7/CHD1 cell lines were generated via transduction of PC3 cells with lentiviral vectors as previously described (Rodrigez et al. Cancer Res 2015;75:1021–34). Cells were mock-infected or infected with M51R mutant vesicular stomatitis virus at a multiplicity of 10 pfu/cell for 6 hours. Mock-infected and virus-infected cells were analyzed in separate experiments.

value: prostate cancer cells

tag: virus


title: Dev_30

description: Starvation 30 minutes


title: Dev_10

description: Starvation 10 hours


title: 4c_shMAP3K7_shCHD1_viral_replicate 3


title: Dorsal root ganglion cells-Control_rep4

value: untreated


title: 4a_shMAP3K7_shCHD1_viral_replicate 1


title: KO_MI5: heart ACKR4_KO mice replicate 2

description: ACKR4_KO mice replicate 2


title: 350

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: ACLF

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

extract_protocol:
Neutrophils were isolated (using Ficoll, Dextran and water to lyse the red cells) from whole blood of 5 healthy subjects, 5 patients with stable cirrhosis and 5 patients with ACLF.  RNA was then extracted and amplified
RNA was extracted using chloroform, isopropanol and ethanol

value: neutrophils

tag: stage of cirrhosis

value: ACLF

tag: disease state

value: Patient with ACLF that is related to sepsis


title: WT_MI6: heart WT mice replicate 3

description: WT mice replicate 3

value: heart

value: wild type


title: LOG OX1_Replicate 3

city: Thiruvananthapuram

first: Saraswati

last: Nayar

state: Kerala

address: Thycaud Post, Poojappura

country: India

institute: Rajiv Gandhi Centre for Biotechnology

data_processing:
The raw data generated was checked for the quality using FastQC2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Pre-processing of the data is done with Trimgalore3 (https://www.encodeproject.org/software/trim_galore).
HISAT-24 which is a splice aligner (Kim et al., 2015) was used to align the high-quality reads to the reference Chlorella variabilis NC64A genome (https://www.ncbi.nlm.nih.gov/genome/?term=Chlorella+variabilis+NC64A) downloaded from NCBI database with the default parameters.
HTSeq was used to estimate and calculate gene abundance (Anders et al., 2015). Absolute counts for each gene were identified, which were used in differential expression calculations.
Genome_build: GCA_000147415.1 v 1.0  (https://www.ncbi.nlm.nih.gov/genome/?term=Chlorella+variabilis+NC64A)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Chlorella variabilis

source_name: Algal cell culture

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen, USA) from 14 dpi (days post inoculation) Chlorella variabilis cells (WT and LOG OX1, three biological replicates each) as per the manufacturer’s protocol.
RNA sequencing libraries were prepared with Illumina-compatible NEB Next® Ultra™ II Directional RNA Library Prep Kit (New England Bio Labs, USA) following manufacturer’s instructions.

value: 14 days post inoculation culture

tag: time harvested

value: 1 hour before dark phase

value: Overexpressor LOG OX1


title: WT_MI5: heart WT mice replicate 2

description: WT mice replicate 2

value: 8-10 weeks


title: 3c_control_shCHD1_viral_replicate 3

tag: cell type

value: Control


title: 346


title: 368


title: 35


title: KO_MI4: heart ACKR4_KO mice replicate 1

description: ACKR4_KO mice replicate 1


title: LOG OX1_Replicate 2


title: WT_MI3: heart WT mice replicate 1

description: WT mice replicate 1


title: 3a_control_shCHD1_viral_replicate 1


title: LOG OX1_Replicate 1


title: 3b_control_shCHD1_viral_replicate 2


title: 1D8

description:
Starved 8 hours
Experiment 2

source_name: Dictyostelium discoideum

tag: treatment

value: Starved 8 hours


title: 1D0-5

description:
Starved 30 minutes
Experiment 2

value: Starved 30 minutes


title: Wild Type_Replicate 3

tag: genotype

value: Wild type


title: Wild Type_Replicate 2


title: Dorsal root ganglion cells-SNI 6h_rep2 [CHFPE190313002_S2_L004]

description:
CHFPE190313002_S2_L004
processed data file:
raw_UMI_counts_2.txt
raw_UMI_counts_2_metadata.txt

data_processing:
Basecalls were performed using bcl2fastq2-v2.19.1.403
Sequenced reads of 10x genomics were processed using Cell Ranger (version.2.1.0) with default parameters
Sequenced reads of Smart-seq2 were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit (version 0.0.13), then mapped to mm10 using hisat2 (version: 2.0.4), finally,  the reads counts were normalized to FPKM (Fragments Per Kilobase of exon per Megabase of library size)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values, raw UNI counts for each single cell and cell information

source_name: Dorsal root ganglion cells-SNI 6h

tag: strain

value: SNI 6h

tag: tissue/cell type

value: Dorsal root ganglion cells

value: 10x genomics


title: 2b_shMAP3K7_control_viral_replicate 2

value: prostate cancer cells


title: Dorsal root ganglion cells-Control_rep3 [CHFPE190313001_S1_L004]

description:
CHFPE190313001_S1_L004
processed data file:
raw_UMI_counts_2.txt
raw_UMI_counts_2_metadata.txt

source_name: Dorsal root ganglion cells-Control

value: untreated


title: Wild Type_Replicate 1


title: Dorsal root ganglion cells-SNI 14d [SNI-14d_S98_L001]

description:
SNI-14d_S98_L001
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

source_name: Dorsal root ganglion cells-SNI 14d

value: SNI 14d


title: 2a_shMAP3K7_control_viral_replicate 1


title: 353

source_name: Stable decompensated cirrhosis

value: neutrophils

value: Stable decompensated cirrhosis

value: Patient with stable cirrhosis


title: 1c_control_control_viral_replicate 3


title: 351


title: Mito screen T1015N 2

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_t1015n_2

data_processing:
Adapter trimming was performed using fastp
Reads were mapped to the relevant sgRNA library using hisat2 and a custom genome (fasta) file for each sgRNA library.
BAM files were converted to counts tables using R package `Rsamtools`
Counts were depth normalized and then z-scored using negative controls
Genome_build: Designed sgRNA sequences were used to create a custom fasta file used for alignments.
Supplementary_files_format_and_content: Counts table for each sgRNA

organism: Chlorocebus sabaeus

source_name: VeroE6 cells

growth_protocol: VeroE6 cells expressing Cas9v2 and their respective sgRNA pool were maintained in T150 flasks in 5% FBS.

extract_protocol:
gDNA was extracted from each sample using standard commercial kits (Zymo).
Lentivirally-integrated sgRNAs were PCR amplified from each gDNA sample and sequencing adapters and indices were added.
Targeted (amplicon) sequencing

treatment_protocol: Each culture was treated with the virus indicated in the Characteristics "infection" field above to select for resistance or sensitization sgRNAs.

tag: sgrna pool

value: Mito proteins

value: VeroE6-Cas9 v2

tag: infection

value: MERS T1015N


title: Dorsal root ganglion cells-SNI 7d [SNI-7d_S98_L001]

description:
SNI-7d_S98_L001
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

source_name: Dorsal root ganglion cells-SNI 7d

value: SNI 7d


title: Dorsal root ganglion cells-SNI 24h_rep2 [CHFPE190313003_S3_L004]

description:
CHFPE190313003_S3_L004
processed data file:
raw_UMI_counts_2.txt
raw_UMI_counts_2_metadata.txt

source_name: Dorsal root ganglion cells-SNI 24h

value: SNI 24h


title: Dorsal root ganglion cells-SNI 2d [SNI-2d_S98_L001]

description:
SNI-2d_S98_L001
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

source_name: Dorsal root ganglion cells-SNI 2d

value: SNI 2d


title: 1b_control_control_viral_replicate 2

value: Control


title: 347


title: Mito screen MERS 2

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_mers_2

value: MERS WT


title: 2c_shMAP3K7_control_viral_replicate 3


title: 1a_control_control_viral_replicate 1


title: Dorsal root ganglion cells-Control_rep2 [SNI-0d_S98_L001]

description:
SNI-0d_S98_L001
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt


title: 374

source_name: Healthy subject

value: No

value: Healthy control


title: 355


title: 372


title: Mito screen rcVSV 1

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_rcVSV_1


title: 373prime


title: 4c-shMAP3K7-shCHD1_replicate 3


title: Mito screen IAV 1

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_iav_1

value: IAV-WSN


title: Dorsal root ganglion cells-SNI 24h_rep1 [HFWL201807020268_2]

description:
HFWL201807020268_2
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

value: Dorsal root ganglion cells

value: 10x genomics


title: Mito screen IAV 2

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_iav_2


title: ZGZZC

city: Nanjing

first: linhan

last: li

address: 168 Gushan Road, Dongshan Street, Jiangning District

institute: Affiliated Jiangning Hospital of Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: adjacent tissue

extract_protocol:
Cervical cancer tissues and adjacent tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent (Thermo). Illumina TruSeq Stranded Total RNA with Ribo-Zero (Cat# 20020612) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cervical cancer

value: adjacent tissue


title: Dorsal root ganglion cells-SNI 6h_rep1 [HFWL201807020267_2]

description:
HFWL201807020267_2
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

value: SNI 6h


title: Mito screen EMCV 2

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_emcv_2

value: EMCV


title: Dorsal root ganglion cells-Control_rep1 [HFWL201807020265_2]

description:
HFWL201807020265_2
processed data file:
raw_UMI_counts_1.txt
raw_UMI_counts_1_metadata.txt

value: untreated


title: ZGZCA

source_name: cervical cancer


title: 4a-shMAP3K7-shCHD1_replicate 1

value: prostate cancer cells


title: 4b-shMAP3K7-shCHD1_replicate 2


title: 371

value: neutrophils


title: 3c-control-shCHD1_replicate 3


title: XHXZC


title: 369prime

value: ACLF

value: Patient with ACLF that is related to sepsis


title: 348

value: Stable decompensated cirrhosis

value: Patient with stable cirrhosis


title: Mito screen T1015N 1

description:
CRISPR sgRNAs from gDNA
mito_counts_table.tsv
mito_t1015n_1

value: Mito proteins

value: VeroE6-Cas9 v2

value: MERS T1015N