title: mixed_ctrl_3

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

institute: Indiana University

data_processing:
STAR v2.7.9a
Assembly: mm10
Supplementary files format and content: featureCounts

source_name: kidney

extract_protocol:
Kidneys were snap frozen and RNA was extracted using Zymo Direct-zol RNA kit.
Library preparation was done following the KAPA RNA HyperPrep Kit Technical Data Sheet (total RNA-seq).

value: kidney

value: mixed


title: locked_ctrl_2

status: Public on Jan 20 2024

type: SRA

department: Medicine

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: locked

tag: treatment


title: mixed_ctrl_2


title: 208262 TLR 354 Rkid | 005 | CD45+

city: Cambridge

first: Sandra

last: Petrus-Reurer

address: Box 202, Level E9 Addenbrooke’s Hospital, Hills Road

department: Department of Surgery

country: United Kingdom

institute: University of Cambridge

description:
208262_TLR_354_Rkid_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

data_processing:
PCR reactions were pooled, and pooled libraries were paired-sequenced on an Illumina Next Seq 2000 instrument.
FASTQ files for each sample were converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline.
DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.2.0.111 (Nanostring).
A minimum of 10,000 reads were required for each sample. Probes were checked for outlier status by implementing a global Grubb’s outlier test with alpha set to 0.01.
The counts for all remaining probes for a given target were then collapsed into a single metric by taking the geometric mean of probe counts.
For each sample, an RNA-probe-pool-specific negative probe normalization factor was generated on the basis of the geometric mean of negative probes in each pool.
To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.
Assembly: hg38
Supplementary files format and content: matrix.csv: Q3 normalized signal intensity
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: CD45+ cells

growth_protocol: Paraformaldehyde-fixed frozen blocks

extract_protocol:
For GeoMx DSP sample collections, entire slides were imaged at 20X magnification and morphologic markers were used to select ROI using organic shapes. Automatic segmentation of ROI based on KRT7pos markers were used to define AOIs, allowing to separate tumor cells (KRT7pos) from adjacent stromal cells (KRT7neg). AOIs were then exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 μl of DEPC-treated water.
Spatial Trasncriptomics library were prepared using NanoString human Whole Transcriptome Atlas (WTA) panel probes according to manufacterer's construction.

treatment_protocol: One representative mouse per group was selected, PCO and matrigel-only kidneys were sectioned (5mm) and slides with the NanoString human Whole Transcriptome Atlas (WTA) panel probes overnight, then stained with KRT7 (1:200, abcam, ab215855, clone [KRT7/760]), CD3 (1:100, Origene, UM000048BF, clone [UMAB54]), CD45 (1:200, CST, 13917BF, clone [D9M8I]), in addition to nuclear staining (Syto 83, ThermoFisher Scientific, S11364) as morphology markers to visualize tissue architecture. Stained slides were loaded onto the GeoMx instrument and scanned for region of interest (ROI) selection.

tag: cell type

value: CD45+ cells


title: 208262 TLR 354 Rkid | 007 | CD45+

description:
208262_TLR_354_Rkid_007_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: uneditable_ctrl_3

value: uneditable


title: mixed_ctrl_1


title: uneditable_ctrl_2


title: 208262 TLR 354 Rkid | 006 | CD45+

description:
208262_TLR_354_Rkid_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 004 | CD45+

description:
208262_TLR_354_Rkid_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 003 | CD45+

description:
208262_TLR_354_Rkid_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: locked_IRI_4

value: IRI


title: uneditable_ctrl_1


title: locked_IRI_3


title: 208262 TL Lkid OT TT | 010 | CD45+

description:
208262_TL_Lkid_OT_TT_010_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 001 | CD45+

description:
208262_TLR_354_Rkid_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 010 | KRT+

description:
208262_TL_Lkid_OT_TT_010_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

source_name: KRT+ cells

value: KRT+ cells


title: BEAS-2B-EV-rep1

city: Shanghai

first: Min

last: Huang

address: 555 Zuchongzhi Road, Pudong

department: State Key Laboratory of Drug Research

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited xlsx file includes TPM values for each Sample

source_name: lung

growth_protocol: BEAS-2B bronchial epithelial cells were maintained in RPMI-1640 supplemented  with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions
RNA-seq transcriptome librariy was prepared following Illumina® Stranded  mRNA Prep, Ligation from Illumina (San Diego, CA) using  1μg of total RNA.

value: lung

tag: cell line

value: bronchial epithelial cells

value: EV


title: locked_IRI_1


title: locked_ctrl_3


title: 208262 TL Lkid OT TT | 009 | CD45+

description:
208262_TL_Lkid_OT_TT_009_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: mixed_IRI_4


title: 208262 TL Lkid OT TT | 009 | KRT+

description:
208262_TL_Lkid_OT_TT_009_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 008 | CD45+

description:
208262_TL_Lkid_OT_TT_008_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: locked_ctrl_1


title: mixed_IRI_2


title: 208262 TL Lkid OT TT | 008 | KRT+

description:
208262_TL_Lkid_OT_TT_008_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 007 | CD45+

description:
208262_TL_Lkid_OT_TT_007_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: uneditable_IRI_4


title: 208262 TL Lkid OT TT | 007 | KRT+

description:
208262_TL_Lkid_OT_TT_007_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: uneditable_IRI_3


title: 208262 TL Lkid OT TT | 006 | CD45+

description:
208262_TL_Lkid_OT_TT_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 005 | KRT+

description:
208262_TL_Lkid_OT_TT_005_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 002 | CD45+

description:
208262_TLR_354_Rkid_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: mixed_IRI_1


title: locked_IRI_2


title: B4

city: shanghai

first: Yunqian

last: Zhang

address: 1665 Kong Jiang Road, Yangpu District

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China.

data_processing:
CLC Genomics Workbech v11.0.1
Sequence reads were trimmed for adaptor sequence/low -quality sequnce using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mappaed to GrCM38/mm 10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8
Read count extraction and normalization were peformed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples
Supplementary files format and content: tab-delimited text files include count values for all Samples

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequnceing libaries
RNA libraries for RNA-seq were prepared using SMRTER mRNA-seq Library Prep Kit following manufacturer's protocols

value: tissue

value: widetype


title: B3


title: 208262 TL Lkid OT TT | 005 | CD45+

description:
208262_TL_Lkid_OT_TT_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 004 | KRT+

description:
208262_TL_Lkid_OT_TT_004_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 004 | CD45+

description:
208262_TL_Lkid_OT_TT_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 006 | KRT+

description:
208262_TL_Lkid_OT_TT_006_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: A4

value: LPS


title: B2


title: 208262 TL Lkid OT TT | 003 | CD45+

description:
208262_TL_Lkid_OT_TT_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: uneditable_IRI_2


title: B1


title: 208262 TL Lkid OT TT | 003 | KRT+

description:
208262_TL_Lkid_OT_TT_003_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TL Lkid OT TT | 002 | CD45+

description:
208262_TL_Lkid_OT_TT_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: A2


title: A3


title: 208262 TL Lkid OT TT | 001 | CD45+

description:
208262_TL_Lkid_OT_TT_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: uneditable_IRI_1


title: 207379 TL Lkid TTOT | 006 | CD45+

description:
207379_TL_Lkid_TTOT_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

value: Autologous


title: cKO1

city: xuzhou

first: Jie

last: Zhao

address: xuzhou city

institute: xuzhou medical university

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: BMDM

extract_protocol:
RNA was havested using TRIzol .1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturers protocols.

value: BMDM


title: cKO2


title: cKO3


title: 207379 TL Lkid TTOT | 005 | KRT+

description:
207379_TL_Lkid_TTOT_005_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 006 | KRT+

description:
207379_TL_Lkid_TTOT_006_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 005 | CD45+

description:
207379_TL_Lkid_TTOT_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: WT 2

value: wild type


title: WT 3


title: WT 1


title: 207379 TL Lkid TTOT | 004 | CD45+

description:
207379_TL_Lkid_TTOT_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: mixed_IRI_3


title: 208262 TL Lkid OT TT | 002 | KRT+

description:
208262_TL_Lkid_OT_TT_002_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 002 | KRT+

description:
207379_TL_Lkid_TTOT_002_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 002 | CD45+

description:
207379_TL_Lkid_TTOT_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 003 | CD45+

description:
207379_TL_Lkid_TTOT_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 003 | KRT+

description:
207379_TL_Lkid_TTOT_003_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 001 | CD45+

description:
207379_TL_Lkid_TTOT_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 207379 TL Lkid TTOT | 001 | KRT+

description:
207379_TL_Lkid_TTOT_001_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 009 | CD45+

description:
203714_TR1_009_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: A1


title: 203714 TR1 | 009 | KRT+

description:
203714_TR1_009_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: SN250_Ear_6

type: RNA

city: Iowa City

first: Rohan

middle: S.

last: Wakade

state: Iowa

address: 25, South Grand Avenue, 2020 MedLabs, Department of Pediatrics

department: Department of Pediatrics

institute: University of Iowa

hyb_protocol: Default nCounter Sprint Profiler Protocol

scan_protocol: Samples were processed on a nCounter Digital Analyzer

data_processing:
RCC files for each sample were imported into nSolver software to determine the quality control metrics. Using the negative probe set the background values were defined and use as a background threshold and this value is subtracted from the raw counts. The resulting background subtracted total raw RNA counts were first normalized against the highest total counts from the biological triplicates and then to the highest total counts for the samples. The statastical significance of changes in gene expression was determined using Benjamini-Hochberg method at an FDR of 0.1
Background subtracted counts were normalized against the highest total counts from the biological replicates.
The resulting values were then averaged and further normalized to highest counts for the samples

organism: Candida albicans

source_name: in vivo C. albicans cells

growth_protocol: For in vitro filament induction, C. albicans strains were inoculated overnight at 30C in YPD media, harvested, and diluted into RPMI + 10% Serum at a 1:50 ratio and incubated for 4 hours at 37C

extract_protocol:
For in vitro filament induction samples, after 4hr induction at 37 degree celsius , cells were collected and RNA was extracted according to the manufacturer protocol for MasterPure Yeast RNA Purfification Kit
For in vivo C. albicans cells, after 24 hours post injections, mouse was euthanized and infected ear was excised and the total RNA was extracted using first Trizol method followed by Qiagen RNeasy kit

value: in vivo C. albicans cells

tag: growth condition

value: cells were inoculated intra-dermally into the mouse ear for 24 hours


title: SN250_Ear_5


title: SN250_Ear_2


title: SN250_Ear_1


title: SN250_Ear_3


title: SN250_Ear_4


title: nrg1ΔΔ-78048_EAR_3


title: nrg1ΔΔ-78048_EAR_2


title: nrg1ΔΔ-78048_EAR_1


title: 78048_EAR_3

value: Clinical strain


title: 203714 TR1 | 007 | CD45+

description:
203714_TR1_007_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 007 | KRT+

description:
203714_TR1_007_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 008 | KRT+

description:
203714_TR1_008_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 008 | CD45+

description:
203714_TR1_008_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 006 | CD45+

description:
203714_TR1_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 005 | CD45+

description:
203714_TR1_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 005 | KRT+

description:
203714_TR1_005_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 78048_EAR_1


title: nrg1ΔΔ-78042_EAR_3


title: 203714 TR1 | 006 | KRT+

description:
203714_TR1_006_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-78042_EAR_1


title: nrg1ΔΔ-78042_EAR_2


title: 203714 TR1 | 004 | CD45+

description:
203714_TR1_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 78042_EAR_3


title: 203714 TR1 | 004 | KRT+

description:
203714_TR1_004_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 78042_EAR_2


title: 78042_EAR_1


title: 203714 TR1 | 003 | KRT+

description:
203714_TR1_003_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 002 | CD45+

description:
203714_TR1_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR1 | 003 | CD45+

description:
203714_TR1_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-78048_R+S_3

source_name: Filamentous cells

value: Filamentous cells


title: 203714 TR1 | 002 | KRT+

description:
203714_TR1_002_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-78048_R+S_1


title: 78048_EAR_2


title: 203714 TR1 | 001 | CD45+

description:
203714_TR1_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

value: CD45+ cells


title: 203714 TR1 | 001 | KRT+

description:
203714_TR1_001_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-78042_R+S_3


title: nrg1ΔΔ-78042_R+S_2


title: nrg1ΔΔ-78048_R+S_2


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 5

city: Beijing

first: Jianan

last: Wang

address: dongdan san tiao number 5

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College

data_processing:
CLC Genomic Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality read filtering  using CLC Genomics Workbench (Quality limit: 0.05)
Trimmed sequence reads mapped to the rat genome (Rat rno7.2) using HISAT2 (version 2.1.0)
HTSeq (version 0.11.2) was used to calculate gene expression read counts
Assembly: Rat rno7.2
Supplementary files format and content: tab-delimited text files include RPKM values for eack Sample

organism: Rattus norvegicus

source_name: cardiac muscles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraies.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,  Catalog #: E7530L) following manufacturer’s recommendation

value: cardiac muscles

tag: strain

value: SD

value: high altitudes at 5000m


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 6


title: nrg1ΔΔ-78042_R+S_1


title: 203714 TR Rkid TT OT | 010 | CD45+

description:
203714_TR_Rkid_TT_OT_010_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 4


title: nrg1ΔΔ-57055_R+S_3


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 3


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 2


title: 203714 TR Rkid TT OT | 009 | CD45+

description:
203714_TR_Rkid_TT_OT_009_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-57055_R+S_2


title: 203714 TR Rkid TT OT | 008 | CD45+

description:
203714_TR_Rkid_TT_OT_008_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: Cardiac muscles, high altitudes at 5000m, 14 days, rep 1


title: Cardiac muscles, normoxia 10m, 14 days, rep 6

value: normoxia


title: nrg1ΔΔ-57055_R+S_1


title: nrg1ΔΔ-94015_R+S_3


title: Cardiac muscles, normoxia 10m, 14 days, rep 5


title: Cardiac muscles, normoxia 10m, 14 days, rep 4


title: Cardiac muscles, normoxia 10m, 14 days, rep 2


title: Cardiac muscles, normoxia 10m, 14 days, rep 3


title: Cardiac muscles, normoxia 10m, 14 days, rep 1


title: 208262 TL Lkid OT TT | 001 | KRT+

description:
208262_TL_Lkid_OT_TT_001_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

value: KRT+ cells


title: 203714 TR Rkid TT OT | 006 | CD45+

description:
203714_TR_Rkid_TT_OT_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: nrg1ΔΔ-94015_R+S_2


title: Standard _secondary heat step_microchem

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38 with TdTomato reporter
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

molecule: polyA RNA

growth_protocol: The human induced pluripotent stem cell (iPSC) line, SPC2-ST-B2, engineered to carry a tdTomato reporter targeted to one allele of the endogenous SFTPC locus (Hurley et al., 2020), underwent directed differentiation to generate iPSC-derived alveolar epithelial type II like cells (iAT2s) in 3D Matrigel cultures using methods we have previously published (Jacob et al., 2017; Jacob et al., 2019). As previously described (Jacob et al., 2017) we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors as follows. In short, cells maintained on mTESR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent (GCDR) and passaged into 6 well plates pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation medium (cSFDM) base as previously described (Jacob et al., 2017) supplemented with 10 µm SB431542 (‘‘SB’’; Tocris) and 2 µm Dorsomorphin (‘‘DS’’; Stemgent). For the first 24 hr after passaging, 10 µm Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (72 hr), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media for 9-11 days. ‘‘CBRa’’ media consists of cSFDM containing 3 µm CHIR99021 (Tocris), 10 ng/mL recombinant human BMP4 (rhBMP4, R&D Systems), and 100nM retinoic acid (RA, Sigma), as previously described (Jacob et al., 2017). On day 15 of differentiation, live cells were sorted on a high-speed cell sorted (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., 2017). Sorted day 15 progenitors were then resuspended in undiluted growth factor-reduced Matrigel (Corning) and distal/alveolar differentiation of cells was performed in ‘‘CK+DCI’’ medium, consisting of cSFDM base, with 3 µm CHIR99021, 10 ng/mL rhKGF, and 50 nM dexamethasone (Sigma), 0.1mM8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1mM3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI) with a brief period of CHIR99021 withdrawal on days 31-35 to achieve iAT2 maturation. To establish pure cultures of iAT2s, cells were sorted by flow cytometry to isolate SFTPC-tdTomato+ cells on day 41 and again on day 69 of differentiation. iAT2s were then maintained through serial passaging as self-renewing monolayered epithelial spheres (“alveolospheres”) by plating in Matrigel (Corning) droplets at a density of 400 cells/μl with refeeding every other day in CK+DCI medium as previously published (Jacob et al., 2019). iAT2 culture quality and purity was monitored at each passage by flow cytometry, with >80% of cells expressing SFTPC-tdTomato over time, as we have previously detailed (Hurley et al., 2020; Jacob et al., 2019). Human iPSC-derived alveolar epithelial type II cells were plated at air-liquid interface culture as detailed (Abo et al., 2022).

extract_protocol:
Human iPSC-derived alveolar epithelial type II cells were dissociated using dispase and trypsin, and FACS-sorted on calcein blue-positive live cells using a Mo-Flo Astrios Cell Sorter.
10X Chromium System, with altered variables: addition of a secondary heat step during cDNA synthesis, and thawing of sample in secondary container of 5% MicroChem Plus prior to adding Recovery Agent

tag: condition

value: Additional secondary heat step, with sample thaw into 5% MicroChem Plus prior to the addition of Recovery Agent

value: iPSC-derived alveolar epithelial type II-like cells


title: nrg1ΔΔ-94015_R+S_1


title: 78048_R+S_3


title: 203714 TR Rkid TT OT | 004 | CD45+

description:
203714_TR_Rkid_TT_OT_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: prefrontal cortex, AD and non-diseased control brains, snRNA-seq

city: London

first: Paul

middle: M

last: Matthews

address: White City

institute: Imperial College London

description: 10X Genomics

data_processing:
Locally generated snRNASeq data were pre-processed using 10X Genomics Cell Ranger. Illumina sequencing files were aligned to the genomic sequence (introns and exons) using GRCh38 annotation in Cell Ranger v3.1. Nuclei were identified above background by the Cell Ranger software.
Assembly: GRCh38
Supplementary files format and content: count data and associated metadata

source_name: Brain

extract_protocol:
Samples from the prefrontal cortex were processed for microvessel single nuclei isolation. All steps were carried out on ice or at 4oC. Tissue was processed to first isolate microvessels and then to release single nuclei for sequencing. Tissue was dounce homogenized and then centrifuged at 1000g for 3 min. Pellets were re-suspended in 5.3% dextran and overlayed on a pre-prepared dextran gradient (4%, 12%, 16%). After centrifugation the bottom layer was subject to a second dextran gradient spin, 4200g for 20 min. The pellets were resuspended and passed through a 100um filter and then a 40um filter. The 40um filter was inverted and centrifuged at 800g for 8 minutes. The isolated microvessels were incubated with Collagenase for 20 minutes and nuclei released by grinding with a pestle and filtering through a 20um filter.
Sorted nuclei were centrifuged at 500 g, resuspended in 50 μl PBS buffer and counted in a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems, L20001) using Acridine Orange dye to stain nuclei. Sufficient nuclei were added for a target of 7,000 nuclei for each library prepared. Barcoding, cDNA synthesis and library preparation were performed using 10X Genomics Single Cell 3’ Gene Expression kit v3 with 8 cycles of cDNA amplification, after which up to 25 ng of cDNA was taken through to the fragmentation reaction and a final indexing PCR was carried out to 14 cycles. cDNA concentrations were measured using Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851), and cDNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, 5067-4627). Samples were pooled to equimolar concentrations and the pool sequenced across 24 lanes of an Illumina HiSeq 4000 according to the standard 10X Genomics protocol.

value: Brain

value: Endothelial cell

tag: disease state

value: mixed sample (AD and control)


title: 203714 TR Rkid TT OT | 005 | CD45+

description:
203714_TR_Rkid_TT_OT_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: Standard_secondary heat step

description: 10x Genomics

value: Additional secondary 60C heat step of 30 mins during cDNA synthesis


title: 78048_R+S_1


title: 78048_R+S_2


title: 203714 TR Rkid TT OT | 002 | CD45+

description:
203714_TR_Rkid_TT_OT_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: Standard

description: 10x Genomics

value: Standard 10X Chromium scRNA-seq pipeline


title: 203714 TR Rkid TT OT | 003 | CD45+

description:
203714_TR_Rkid_TT_OT_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 TR Rkid TT OT | 007 | CD45+

description:
203714_TR_Rkid_TT_OT_007_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 24hpfEmbryo_FedFather_Rep6

city: Birmingham

first: Ada

last: Jimenez-Gonzalez

address: 1, Vincent Drive

institute: University of Birmingham

data_processing:
Following Lexogen guidelines, sequencing adapters, polyA read through and low-quality tails were removed by using the bbduk tool of the bbmap package (parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=r, trimq=10, minlength=20) (Bushnell, 2014). RNA-seq reads were then mapped to the zebrafish reference genome (GRCz11.96) using STAR with default parameters (version: 2.6.0c) (Dobin et al., 2023). Gene expression levels were estimated by the read counting module embedded within the STAR tool (–quantMode GeneCounts). Differentially expressed genes were identified by using edgeR (10.1093/bioinformatics/btp616) using the TMM method to normalise raw read counts, whereas common, trended and tagwise dispersions were estimated by maximising the negative binomial likelihood (default). Lowly expressed genes were removed (only genes expressed >1 TMM in at least 50% of the samples were retained) and differentially expressed genes were tested performing quasi-likelihood F-tests (glmQLFit and glmQLTest), including the maternal genetic background of each embryo pair in the design of the linear model. Only genes showing FDR < 0.1 were considered as differentially expressed (115 downregulated genes and 30 upregulated). GO enrichment analysis was performed by using topGO (Alexa & Rahnenfuhrer, 2022) on the GO terms associated with the up- and down-regulated genes separately. In both analyses, GO terms associated with genes expressed >1 TMM in at least 50% of the samples were used as background. The statistical significance of the enrichments was tested with a Fisher’s Exact Test (algorithm=’weight’), then, GO terms associated with less than two significant genes were discarded prior to FDR calculation (Benjamini et al., 2023). Significant threshold was imposed to FDR < 0.1.
Assembly: danRer11
Supplementary files format and content: EdgeR TMM normalized counts

organism: Danio rerio

source_name: 24hpf Embryo

extract_protocol:
For transcriptome analysis, we used one to three 24-hpf embryos from each clutch that were manually dechorionated and flash frozen in 1.5 ml Eppendorf tubes. RNA extraction was performed with the RNeasy micro kit (Qiagen) following the manufacturer's instructions. Briefly, samples were lysed in RLT buffer passing the embryos through a needle and syringe. Lysates were passed through a MinElute spin column and centrifuged for 15s at 13000 g. samples were washed with buffer RW1 and treated in-column with DNase I diluted in buffer RDD for 15 minutes at room temperature (RT). The digestion reaction was stopped with RW1 buffer and centrifuge step. Columns were washed with RPE buffer and 80% ethanol followed by a 5 minute centrifuge step to remove any ethanol residues. Finally, we eluted the RNA in 14 μl of elution buffer and proceeded with quality assessment by TapeStation HS RNA tapes (Agilent).
The library preparation was performed with the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). RNA was normalised to 13.5 ng/μl and the RNA input for prep = 67.5 ng per sample. The protocol for high quality samples was used. SIRV set 3 were spiked into the samples at a very low level to allow technical evaluation of library prep and sequencing performance.    18 cycles of PCR were performed. Libraries were quantified with Picogreen assay (Fisher Scientific) and sizes were determined with a HS D1000 tape (Agilent). Libraries were pooled to 4nM final concentration and spiked with 1% phiX and processed on a NextSeq flow cell (150 cycles mid output) for sequencing on a NextSeq 500.

value: 24hpf Embryo

value: AB

tag: group

value: Fed Father


title: 24hpfEmbryo_StarvedFather_Rep5

value: Starved Father


title: 78042_R+S_3

value: Filamentous cells

value: Clinical strain


title: 203714 TR Rkid TT OT | 001 | CD45+

description:
203714_TR_Rkid_TT_OT_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

value: CD45+ cells


title: 203714 BLL TT OT | 010 | KRT+

description:
203714_BLL_TT_OT_010_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 203714 BLL TT OT | 009 | KRT+

description:
203714_BLL_TT_OT_009_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 78042_R+S_1


title: 24hpfEmbryo_FedFather_Rep5


title: 203714 BLL TT OT | 008 | KRT+

description:
203714_BLL_TT_OT_008_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 24hpfEmbryo_StarvedFather_Rep4


title: 57055_R+S_3


title: 24hpfEmbryo_StarvedFather_Rep6


title: 203714 BLL TT OT | 007 | KRT+

description:
203714_BLL_TT_OT_007_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 24hpfEmbryo_FedFather_Rep4


title: WTC11 i3 Neurons, RAL 1 uM

city: Philadelphia

first: Kelly

last: Jordan-Sciutto

state: PA

address: 240 S. 40th St, Levy Building, Room 312

department: Oral Medicine

institute: University of Pennsylvania, School of Dental Medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: The trimmed reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: Tab-delimited text files with raw counts for each sample

source_name: WTC11 NGN2

growth_protocol: Human i3 cortical neurons were generated as previously described (Wang, Ward et al. 2017, Fernandopulle, Prestil et al. 2018). In brief, human iPSCs reprogrammed from a wild type male containing a doxycycline-inducible NGN2 integrated into the AAVS1 safe harbor locus were cultured on matrigel-coated (Corning) plates in supplemented Essential 8 medium (Gibco). Once iPSC cultures reached confluence, they were split and induced toward neuronal differentiation with doxycycline-containing induction media (DMEM/F12-Gibco, N2, & NEAA-Invitrogen) for 3 days. On DIV 3, induced neurons were lifted and plated PEI/Laminin-coated Axion CytoView MEA plates. Neurons were plated at a density of 2x105 cells per ml for MEA experiments. Cells were matured in cortical maturation media (BrainPhys-Stem Cell Technologies, B-27-Gibco, BDNF, NT3, and laminin) for an additional 18 days prior to experiment initiation.

extract_protocol:
Following the completion of MEA experiments, neurons from 6 replicate wells were lysed in the well using TRIzol (Invitrogen) and pooled RNA was isolated using manufacturer protocols. Purity and concentration of RNA were confirmed using Nanodrop, and Zymo RNA Clean & Concentrator-25 was used on any samples that did not pass initial quality control (260/280 > 2, 260/230 > 1.8, minimum concentration 50 ng/µl).
Libraries prepared via Illumina-compatible kit by Azenta/Genewiz using PolyA selection

treatment_protocol: Elvitegravir and raltegravir were resuspended in dimethysulfoxide (DMSO, Veh). Working stocks were prepared via serial dilution in DMSO to ensure all doses (0.1 µM, 1 µM, and 10 µM) contained the same amount of DMSO. i3 neurons were treated with INSTIs beginning on DIV 18 and maintained for 9 days for MEA experiments. Fifty percent media changes every other day were supplemented with an additional half dose of drug to ensure any removed was replaced, but no drug metabolism was assumed. For LPS + ATP samples, uninfected iMg cultures were treated with 1 ng/ml E. coli LPS for 23.5 hours beginning on DPI 8, with a 30 minute addition of 2.5mM ATP prior to supernatant collection. i3 neurons were treated with supernatants at a ratio of 1:4 in cortical maturation media beginning on neuronal DIV 19 and maintained for 4 days.

value: WTC11 NGN2

value: i3 Neuron

value: WT

value: Raltegravir 1 uM


title: 57055_R+S_2


title: WTC11 i3 Neurons, EVG 1 uM

value: Elvitegravir 1 uM


title: WTC11 i3 Neurons, Veh

value: DMSO


title: WTC11 i3 Neurons, RAL 0.1 uM

value: Raltegravir 0.1 uM


title: WTC11 i3 Neurons, Veh iMg Sup

value: WT6 Mock iMg Supernatant


title: 203714 BLL TT OT | 006 | KRT+

description:
203714_BLL_TT_OT_006_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

value: KRT+ cells


title: WTC11 i3 Neurons, EVG 10 uM

value: Elvitegravir 10 uM


title: WTC11 i3 Neurons, LPS iMg Sup

value: WT6 LPS/ATP iMg Supernatant


title: T4

city: shiyan

first: Xueyan

last: Xi

state: Hubei Province

address: Renmin Nanlu #30

department: Immunology

institute: Hubei University of Medicine

description: SLE with PF 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0). Pvalue <0.05 and |FoldChange|≥1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMC)s were isolated from peripheral-blood samples of study participants via density gradient centrifugation using Ficoll-Paque media (Sigma-Aldrich, No. 17144002).

extract_protocol:
We isolated 1×106 PBMCs/mL peripheral blood. Total ribonucleic acid (RNA) was extracted from 3×106 isolated PBMCs using TRIzol reagent (Thermo Fisher Scientific, No. 15596026) per manufacturer’s protocol.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: Systemic lupus erythematosus (SLE) patients who met the American College of Rheumatology Criteria for SLE, were recruited from Renmin Hospital in Shiyan between April, 2020 to October, 2020. They were free from tumors, infections, and other autoimmune diseases.  SLE patients included 3 patients with pulmonary fibrosis (PF) and 3 SLE patients without PF. The diagnosis of PF is based on the results of computed tomography (CT) examination.

tag: gender

value: Female

tag: age

tag: disease

value: Systemic lupus erythematosus patients with pulmonary fibrosis


title: 24hpfEmbryo_StarvedFather_Rep3

value: 24hpf Embryo

value: AB

value: Starved Father


title: 57055_R+S_1

value: Filamentous cells

value: Clinical strain


title: 203714 BLL TT OT | 005 | KRT+

description:
203714_BLL_TT_OT_005_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 24hpfEmbryo_FedFather_Rep3

value: Fed Father


title: T1

description: SLE with PF 1


title: 203714 BLL TT OT | 004 | KRT+

description:
203714_BLL_TT_OT_004_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: C4

description: SLE without PF 3

value: Systemic lupus erythematosus patients without pulmonary fibrosis


title: 78042_R+S_2


title: 24hpfEmbryo_StarvedFather_Rep2


title: SN250_R+S_3

value: Laboratory strain


title: 24hpfEmbryo_FedFather_Rep2


title: 203714 BLL TT OT | 002 | KRT+

description:
203714_BLL_TT_OT_002_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 24hpfEmbryo_StarvedFather_Rep1


title: 203714 BLL TT OT | 001 | KRT+

description:
203714_BLL_TT_OT_001_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: T3

description: SLE with PF 2


title: SN250_R+S_2


title: C2

description: SLE without PF 1


title: 24hpfEmbryo_FedFather_Rep1


title: 94015_R+S_2


title: ZT8, rep3

status: Public on Jan 19 2024

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

data_processing:
Sequence reads and trimmed reads quality control was carried out using FastQC-v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!-v0.6.6 (parameter - Phred33 quality limit: 20)
Trimmed sequence reads were mapped to M27 Gencode reference genome (GrCM39) and read counts per transcript obtained using Salmon-v1.6.0 in mapping-based mode (parameters- gcBias, seqBias)
Salmon output files were imported and converted for DESeq2 using Tximeta-v1.12.4
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2
Normalised counts were generated using the median of ratios method in DESeq2.
Assembly: M27
Supplementary files format and content: csv file represents TPM, produced by Salmon, and summarized to gene level via DESeq2

source_name: L4-6 DRG

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Signle Cell/Low Input RNA Library Prep kit following manufacturer's protocols.

treatment_protocol:
L4-6 DRGs were dissected at ZT8 or ZT20.
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population

value: L4-6 DRG

tag: Sex

value: Male

value: 6-8 weeks

tag: time


title: ZT8, rep2


title: ZT8, rep1


title: 94015_R+S_1


title: ZT20, rep3


title: ZT20, rep4


title: 203714 BLL TT OT | 003 | KRT+

description:
203714_BLL_TT_OT_003_KRT
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: C3

description: SLE without PF 2


title: ZT20, rep2


title: Population Hi-C EED KO 24h_replicate 2

first: David

last: Lando

address: Department Biochemistry , Sanger Bulding, Tennis Court Road

department: Biochemistry

library_source: genomic

data_processing:
Single-cell Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Population Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to remove PCR redundancy in amplified RE1-RE1 ligation events to create a single list of paired RE1 fragment ends.
Assembly: mm10

molecule: genomic DNA

source_name: diploid EED knock out mESC derived from strain E14

growth_protocol: For routine cell culture, cell lines were maintained in N2B27 media supplemented with 2i and mouse leukemia inhibitory factor (mLIF). 50 % DMEM/F-12 medium (Gibco, 21041025) and 50 % Neurobasal™ Medium (Gibco, 12348017) was supplemented with 1 x N2 to a final concentration of 2.5 µg/ml insulin (provided in-house by the Cambridge Stem Cell Institute), 0.5x B-27™ Supplement (Gibco, 17504044), 1x minimum essential medium non-essential amino acids supplement (Sigma-Aldrich, M7145), 2 mM L-glutamine (Life tech, 25030024), and 0.1 mM 2-mercaptoethanol (Life tech, 21985023), 2i inhibitors (1 µM PD0325901, 3 µM CHIR99021) and 10 ng/ml mLIF (provided by the Biochemistry Department, University of Cambridge). Cells were routinely screened for mycoplasma contamination.

extract_protocol:
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Population Hi-C libraries were prepared using an adaptor ligation method. Briefly, sonicated blunt-ended biotinylated junctions of ~300 bp in size were captured on streptavidin M-280 dynabeads. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 8-10 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were purified using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.
Population Hi-C

treatment_protocol: Naïve ES state cells were plated at a density of 10,000 cells/cm2 and grown in N2B27 with 2i and LIF for 48 hrs. 24 hr state cells were plated at the same density in N2B27 with 2i and no LIF. After 24 hrs the two inhibitors were removed and cells were grown in N2B27 only media for a further 24 hrs. To obtain 24 hr Rex1 High and 24hr Rex1 Low/formative state cells cells at the 24 hr stage were FACS sorted with gates set to collect cells with the highest and lowest 25% GFP expression, repectively. 48 hr primed state cells were plated and grown in the same way except that after removal of the two inhibitors cells were grown in N2B27 only media for 48 hrs.

value: targeted knock out of EED gene

value: 24 hr


title: RNASeq_NA1000_DkdpE_2_Low_K

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

data_processing:
Between 2 x 10^7 and 3 x 10^7 paired-end sequence reads (2 x 100) were first mapped on the genome of C. crescentus NA1000 (NC_011916.1) using Galaxy
The number of reads overlapping each genomic position was computed using Galaxy
A DESeq2 analysis was then peformed between the WT and DchvI samples using Galaxy
Assembly: NC_011916.1
Supplementary files format and content: The xls file reports K+-dependent regulon with Fold Change (FC) between WT high (5 mM) and low (0.025 mM) K+. The different columns are organized as follows: column 1: Gene_ID (CCNA gene identification number); column 2: Name (Predicted function of the corresponding gene); column 3: Base_mean (mean of normalized counts); column 4: log2[FC_WT_High_K/WT_Low_K] (base 2 log of fold change between WT_High_K and WT_Low_K); column 5: P-value; column 6: P-adj (adjusted P-value); column 7: FC_WT_High_K/WT_Low_K (fold change between WT_High_K and WT_Low_K) ; column 8: -(log_FDR) (-base10 log of false discovery rate)
Supplementary files format and content: The xls file reports K+- and KdpE-dependent regulon with Fold Change (FC) between WT and DkdpE strains at low (0.025 mM) K+. The different columns are organized as follows: column 1: Gene_ID (CCNA gene identification number); column 2: Name (Predicted function of the corresponding gene); column 3: Base_mean (mean of normalized counts); column 4: log2[FC_WT_Low_K_DkdpE_Low_K] (base 2 log of fold change between WT_Low_K and DkdpE_Low_K) ; column 5: P-value; column 6: P-adj (adjusted P-value); column 7:  FC_WT_Low_K/DkdpE_Low_K (fold change between WT_Low_K and DkdpE_Low_K) ; column 8: -(log_FDR) (-base10 log of false discovery rate)

organism: Caulobacter vibrioides

source_name: Mid-exponential phase

growth_protocol: C. crescentus strains grown overnight at 30°C in minimal media(M2G) to saturation before being diluted in fresh M2G-K containing either 5 mM K+ or 0.025 mM K+ and grown at 30°C to mid-exponential phase (OD660~0.3).

extract_protocol:
Total RNA was extracted with RNeasy® Protect Bacteria Kit from Qiagen and following manufacturer’s instructions.
RNA-Seq libraries were prepared at the Seqalis company (Belgium) using the RNASeq TTRNA library according to the manufacturer's instructions, after rRNA depletion and cDNA synthesis.

value: Mid-exponential phase

value: DkdpE

value: Mid-exponential phase in synthetic minimal medium M2G-K + 0.025 mM K+


title: Population Hi-C EED KO ES replicate 1

value: diploid EED knock out mESC derived from strain E14

value: Naïve ES


title: RNASeq_NA1000_1_High_K

value: WT

value: Mid-exponential phase in synthetic minimal medium M2G-K + 5 mM K+


title: RNASeq_NA1000_2_High_K


title: RNASeq_NA1000_1_Low_K


title: WT

data_processing:
Around 2 x 10^7 paired-end sequence reads (2 x 75) were first mapped on the genome of C. crescentus NA1000 (NC_011916.1) and converted to SAM using BWA and SAM tools from the sourceforge server (https://sourceforge.net/)
MACS2 algorithm was used to model the length of DNA fragment as well as the shift size.
The number of reads overlapping each genomic position was computed using custom Python scripts and the previously modeled DNA fragment and shift sizes.
A peak was defined as the genomic region where each position has more reads than the 97th percentile. The candidate peaks were annotated using custom Python scripts.
Assembly: NC_011916.1
Supplementary files format and content: The xls files report KdpE ChIP-Seq peaks in Caulobacter. The  different columns are organized as follows: column 1: Start_Coord (coordinates for the start of the peak); column 2: End_Coord (coordinates for the end of the peak); column 3: Summit (highest number of reads of peak); column 4:  Summit_Coord (coordinates for the highest number of reads of peak); column 5: Reads (number of reads in the peak); column 6: Reads Norm (number of reads / total number of alignedreads ); column 7: GeneUp (CCNA_number of gene upstream of the peak based on the summit); column 8: GeneUpName (name of gene upstream of the peak); column 9: GeneDown ( CCNA_number of gene downstream of the peak based on the summit); column 10: GeneDownName (name of gene downstream of the peak); column 11: OperonUp (Operon in which gene upstream of the peak belongs); column 12: OperonDown (Operon in which gene downstream of the peak belongs).

source_name: mid-exponential phase

growth_protocol: C. crescentus strains grown overnight at 30°C in synthetic media (M2G) to saturation before being diluted in fresh M2G media and grown at 30°C to mid-exponential phase (OD660~0.5-0.6).

extract_protocol:
Resuspended pellets were lysed with 2 µl of Ready-lyse lysozyme solution (Epicentre)  for 5 min at RT. Protease inhibitors (Roche) was added and incubated for 10 min. Then, 550 µl of ChIP buffer (1.1% triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, plus protease inhibitors) was added to the lysate and incubated at 37 °C for 10 min before sonication (2 x 8 bursts of 30 sec on ice using a Diagenode Bioruptor) to shear DNA fragments to a length of 300 to 500 bp. Lysate was cleared by centrifugation for 10 min at 12,500 rpm at 4 °C and protein content was evaluated by measuring OD280. Then, 7.5 mg of proteins were diluted in ChIP buffer supplemented with 0.01% SDS and precleared 1 h at 4 °C with 50 µl of protein A agarose beads (BioRad) and 100 µg BSA. One µl of polyclonal anti-ChvI antibodies, produced by rabbits (CER Groupe, Marloie, Belgium) immunised with purified His6-ChvI protein, were added to the supernatant before overnight incubation at 4 °C under gentle agitation. Eighty µl of BSA pre-saturated protein A agarose beads were added to the solution for 2 h at 4 °C with rotation, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), once with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA) at 4 °C and a second wash with TE buffer at RT. The DNA-protein complexes were eluted twice in 250 µl freshly prepared elution buffer (0.1 M NaHCO3, 1% SDS). NaCl was added at a concentration of 300 mM to the combined eluates (500 µl) before overnight incubation at 65 °C to reverse the crosslink. The samples were treated with 20 µg of proteinase K in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5) for 2 h at 45 °C. DNA was extracted using Nucleospin PCR clean-up kit (Macherey-Nagel) and resuspended in 50 µl elution buffer (5 mM Tris-HCl pH 8.5).
ChIP-Seq libraries were prepared at the Seqalis company (Belgium) using the Illumina TruSeq DNA library (Roche-KapaHyperPrep)  according to the manufacturer's instructions.

treatment_protocol: 80 ml of mid-log phase cells (OD660~ 0.5-0.6) were cross-linked in 1% formaldehyde and 10 mM sodium phosphate (pH 7.6) at room temperature for 10 min and 30 min on ice thereafter. Crosslinking was stopped by addition of 125 mM glycine and incubated for 5 min on ice. Cells were washed thrice in PBS resuspended in 450 µl in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl)

value: mid-exponential phase

value: {delta}kdpE PxylX::kdpE

value: Mid-exponential phase in synthetic minimal medium (M2G-K) with 0.025 mM K+


title: RNASeq_NA1000_DkdpE_1_Low_K


title: Population Hi-C EED KO 24h replicate 1


title: DkdpD

value: {delta}kdpDE PxylX::kdpE


title: RNASeq_NA1000_2_Low_K


title: Population Hi-C EED KO ES replicate 2


title: SN250_R+S_1

value: Filamentous cells

value: Laboratory strain


title: ChIP input K27ac K4me3 K9me3 48h replicate 2

data_processing:
Single-cell Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Population Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to remove PCR redundancy in amplified RE1-RE1 ligation events to create a single list of paired RE1 fragment ends.
ChiP-seq paired-end reads were first mapped to the mouse genome reference sequence GRCm38/mm10 using Bowtie 2 v2.1.038 and filtered to retain reads with a mapping quality >30 using Samtools39. Peaks were called using MACS2 v2.1. Model-based analysis of ChIP-Seq data was carried out using MACS2 with a minimum FDR cut-off of 0.01 (-q 0.01) to find narrowPeaks (except for H3K9me3 and H3K27me3 which have broad peak features). For samples with the Drosophila spike-in, reads were mapped to the Drosophila genome (release 6/dm6) using Bowtie 2, but with a mapping quality cut-off equal to 10. The Drosophila spike-in read count was quantified using the Samtools Flagstat module. Bigwig files were normalised using the corresponding Drosophila spike-in read abundance with the –extendReads option in deepTools40.
Single-cell RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 with the GSNAP aligner (gmap-2014- 12-17) using the parameters -n 1 -N 1 for uniquely mapped reads and allowing for novel splicing sites. Gene read counts were assigned using HTSeq (v0.6.1) based on gene annotation from ensemble release 81. A quality control filtering was then applied to the cells using the R package Scater (1.2.0) : more that 5*10^5 reads per cell, more than 7000 individual features detected and less than 20% of the reads mapping to mitochondrial genes. The reads were then normalised for library size using the R package Scran (1.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: The Hi-C ncc file (.ncc) is a tab-separated text format file containing the Hi-C contacts for either single cell or population Hi-C samples. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2 seq_pos_2
Supplementary files format and content: The n3d.txt (.n3d.txt) file format for single cell genomic 3D structure coordinate positions is a  simple whitespace-separated text format consisting of blocks of lines for separate  chromosomes. Each block consists of a header  line, giving the chrosome name, number of coordinates (i.e. number of particle  positions) and the number of alternative coordinate models. The subsequent  particle data lines for the chromosome contain the basebair sequence position  followed by cartesian (X, Y, Z) coordinates for each alternative model.
Supplementary files format and content: The bigWig (.bw) files are in an indexed binary format suitable for displaying data in a Genome Browser. No bigWig files for Input samples.
Supplementary files format and content: The peak files (.narrowPeak and .broadPeak) are files that contain called peaks of signal enrichement based on pooled, normalized data.The .narrowPeak files are in a BED6+4 format while the .broadPeak files are in a BED 6+3 format. No peak files for Input samples
Supplementary files format and content: The single-cell RNA-seq sample and barcode file (.samplebarcode.csv) is a file that lists all 96 cell sample names and there corresponding barcode name and sequence.
Supplementary files format and content: The single-cell RNA-seq expression read file (.tsv) is a file that lists the gene exprerssion read count for each different cell. The first column is the ensembl gene id. The remaining columns are the expression read counts for each individual cell.

source_name: Yes

extract_protocol:
Briefly, cells on dishes were fixed in media containing 1 % formaldehyde for 10 min at room temperature. Fixing was quenced by adding glycine to a final concentration of 150 mM. Cell nuclei were made by resuspending at 2x107 cells /ml with lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, protease inhibitors) on ice. After a gentle spin (600g, 5 minutes, 4 degrees) nuclei were pelleted and then used for ChIP.
ChIP-seq libraries were prepared using the NEXTflex Rapid DNA-seq kit (Illumina)

value: Yes

value: diploid wild type mESC derived from strain E14

value: wild type

value: 48 hr primed


title: ChIP input K27ac K4me3 K9me3 48h replicate 1


title: ChIP input K27me3 48h replicate 2


title: ChIP input K27ac K4me3 K9me3 ES replicate 1

value: Naive ES


title: ChIP input K27ac K4me3 K9me3 24h replicate 2

value: 24 hr


title: ChIP input K27ac K4me3 K9me3 ES replicate 2


title: ChIP input K27me3 24h replicate 2


title: ChIP input K27ac K4me3 K9me3 24h replicate 1


title: ZT20, rep1

value: L4-6 DRG

value: Male

value: 6-8 weeks


title: ChIP input K27me3 ES replicate 1


title: ChIP input K27me3 ES replicate 2


title: ChIP H3K27ac 48h replicate 2


title: ChIP H3K27ac 24h replicate 1


title: ChIP H3K27ac 24h replicate 2


title: ChIP H3K27ac ES replicate 2


title: ChIP H3K27ac ES replicate 1


title: ChIP H3K27me3 48h replicate 1


title: ChIP H3K27me3 48h replicate 2


title: ChIP H3K9me3 48h replicate 1


title: ChIP input K27me3 48h replicate 1


title: ChIP H3K9me3 48h replicate 2


title: ChIP H3K27me3 24h replicate 1


title: ChIP H3K27me3 ES replicate 2


title: ChIP H3K27me3 ES replicate 1


title: ChIP input K27me3 24h replicate 1


title: ChIP H3K9me3 ES replicate 2


title: ChIP H3K9me3 24h replicate 1


title: ChIP H3K4me3 48h replicate 1


title: ChIP H3K4me3 ES replicate 2


title: ChIP H3K4me3 24h replicate 1


title: ChIP H3K4me3 24h replicate 2


title: ChIP H3K9me3 ES replicate 1


title: ChIP H3K27ac 48h replicate 1


title: Population Hi-C Dnmt3ab KO 24h_replicate 2

extract_protocol:
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Population Hi-C libraries were prepared using an adaptor ligation method. Briefly, sonicated blunt-ended biotinylated junctions of ~300 bp in size were captured on streptavidin M-280 dynabeads. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 8-10 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were purified using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.

value: diploid Dnmt3a and b knock out mESC derived from strain E14

value: targeted knock out of Dnmt3a and Dnmt3b genes


title: ChIP H3K4me3 ES replicate 1


title: Population Hi-C Tet1 KO 24h replicate 2

value: diploid Tet1 knock out mESC derived from strain E14

value: EF1alpha-driven Cas9 cassette targeted to the Rosa26 locus and targeted knock out of Tet1 gene


title: Population Hi-C Tet1 KO ES replicate 2


title: Population Hi-C Dnmt3ab KO ES replicate 2


title: ChIP H3K27me3 24h replicate 2


title: Single nucleus Hi-C cell P30G8

source_name: haploid mESCs derived from strain 129/Ola

extract_protocol:
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Single cell Hi-C libraries were prepared using an adaptor ligation method. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with AluI enzyme to generate blunt ends. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~300-1000 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.
Single-nucleus Hi-C

value: Naïve ES


title: Population Hi-C WT 24h replicate 2

value: EF1alpha-driven Cas9 cassette targeted to the Rosa26 locus


title: ChIP H3K9me3 24h replicate 2


title: Population Hi-C WT 24h replicate 1


title: ChIP H3K4me3 48h replicate 2


title: Population Hi-C WT ES replicate 2


title: Single-cell RNA-seq ES

extract_protocol:
Cells were collected from the plate using accutase. The cell suspension was then sorted using a MoFlo cell sorter (Beckman Coulter) in order to recover one cell per well containing 2 μl of cell lysis buffer (0.2% (V/V) Triton-X100 and 2U/uL of RNase inhibitor.
The single-cell RNA-seq library preparation was carried out using the Smart-seq2 protocol described by Picelli et al (2014) Nat. Protoc. 9, 171–181.


title: Population Hi-C WT ES replicate 1


title: Population Hi-C Dnmt3ab KO ES replicate 1


title: Population Hi-C Haploid 24hRexL replicate 2

value: haploid mESCs derived from strain 129/Ola

value: 24 hr Rex1 Low/formative


title: Single-cell RNA-seq 24h

value: Yes


title: Population Hi-C Haploid ES replicate 2


title: Population Hi-C Haploid 48h replicate 2


title: Population Hi-C Tet1 KO ES replicate 1


title: Population Hi-C Haploid 24hRexH replicate 2

value: 24 hr Rex1 High


title: Population Hi-C Tet1 KO 24h replicate 1


title: Population Hi-C Haploid 24hRexL replicate 1


title: Population Hi-C Haploid 48h replicate 1


title: R21873

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

institute: RTI  International

data_processing:
Transcripts were quantified using GENCODE v40 (GRCh38) transcriptome with Salmon (v 1.1.0).
Gene-level quantification was done with the tximport R package (v1.14.2).
Assembly: GRCh38/ GENCODE v40
Supplementary files format and content: compressed tab-deliminated text file including raw counts for each sample

source_name: DLPFC

extract_protocol:
Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Illumina TruSeq Total RNA Stranded RiboZero Gold (Illumina Inc, San Diego, CA) was used for library prep.

value: DLPFC

tag: dsm-5 aud status

value: M

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Control

tag: pmi

tag: rin

tag: sample plate

tag: sample well

tag: brain number


title: R21872

tag: tissue


title: R21871

value: Case


title: R21870


title: Single-cell RNA-seq 12h

data_processing:
Single-cell RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 with the GSNAP aligner (gmap-2014- 12-17) using the parameters -n 1 -N 1 for uniquely mapped reads and allowing for novel splicing sites. Gene read counts were assigned using HTSeq (v0.6.1) based on gene annotation from ensemble release 81. A quality control filtering was then applied to the cells using the R package Scater (1.2.0) : more that 5*10^5 reads per cell, more than 7000 individual features detected and less than 20% of the reads mapping to mitochondrial genes. The reads were then normalised for library size using the R package Scran (1.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: The single-cell RNA-seq sample and barcode file (.samplebarcode.csv) is a file that lists all 96 cell sample names and there corresponding barcode name and sequence.
Supplementary files format and content: The single-cell RNA-seq expression read file (.tsv) is a file that lists the gene exprerssion read count for each different cell. The first column is the ensembl gene id. The remaining columns are the expression read counts for each individual cell.

tag: cell line

tag: cell type

value: diploid wild type mESC derived from strain E14

tag: genotype

value: wild type

tag: treatment

value: 24 hr


title: Population Hi-C Haploid ES replicate 1

value: Naive ES


title: Single nucleus Hi-C cell P54H12

data_processing:
Single-cell Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Population Hi-C paired-end reads were processed using the NucProcessing software package (https://github.com/TheLaueLab/nuc_processing). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to remove PCR redundancy in amplified RE1-RE1 ligation events to create a single list of paired RE1 fragment ends.
ChiP-seq paired-end reads were first mapped to the mouse genome reference sequence GRCm38/mm10 using Bowtie 2 v2.1.038 and filtered to retain reads with a mapping quality >30 using Samtools39. Peaks were called using MACS2 v2.1. Model-based analysis of ChIP-Seq data was carried out using MACS2 with a minimum FDR cut-off of 0.01 (-q 0.01) to find narrowPeaks (except for H3K9me3 and H3K27me3 which have broad peak features). For samples with the Drosophila spike-in, reads were mapped to the Drosophila genome (release 6/dm6) using Bowtie 2, but with a mapping quality cut-off equal to 10. The Drosophila spike-in read count was quantified using the Samtools Flagstat module. Bigwig files were normalised using the corresponding Drosophila spike-in read abundance with the –extendReads option in deepTools40.
Single-cell RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 with the GSNAP aligner (gmap-2014- 12-17) using the parameters -n 1 -N 1 for uniquely mapped reads and allowing for novel splicing sites. Gene read counts were assigned using HTSeq (v0.6.1) based on gene annotation from ensemble release 81. A quality control filtering was then applied to the cells using the R package Scater (1.2.0) : more that 5*10^5 reads per cell, more than 7000 individual features detected and less than 20% of the reads mapping to mitochondrial genes. The reads were then normalised for library size using the R package Scran (1.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: The Hi-C ncc file (.ncc) is a tab-separated text format file containing the Hi-C contacts for either single cell or population Hi-C samples. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2 seq_pos_2
Supplementary files format and content: The n3d.txt (.n3d.txt) file format for single cell genomic 3D structure coordinate positions is a  simple whitespace-separated text format consisting of blocks of lines for separate  chromosomes. Each block consists of a header  line, giving the chrosome name, number of coordinates (i.e. number of particle  positions) and the number of alternative coordinate models. The subsequent  particle data lines for the chromosome contain the basebair sequence position  followed by cartesian (X, Y, Z) coordinates for each alternative model.
Supplementary files format and content: The bigWig (.bw) files are in an indexed binary format suitable for displaying data in a Genome Browser. No bigWig files for Input samples.
Supplementary files format and content: The peak files (.narrowPeak and .broadPeak) are files that contain called peaks of signal enrichement based on pooled, normalized data.The .narrowPeak files are in a BED6+4 format while the .broadPeak files are in a BED 6+3 format. No peak files for Input samples
Supplementary files format and content: The single-cell RNA-seq sample and barcode file (.samplebarcode.csv) is a file that lists all 96 cell sample names and there corresponding barcode name and sequence.
Supplementary files format and content: The single-cell RNA-seq expression read file (.tsv) is a file that lists the gene exprerssion read count for each different cell. The first column is the ensembl gene id. The remaining columns are the expression read counts for each individual cell.
Library strategy: Single-nucleus Hi-C

extract_protocol:
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Single cell Hi-C libraries were prepared using an adaptor ligation method. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with AluI enzyme to generate blunt ends. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~300-1000 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.

value: 48 hr primed


title: R21874


title: R21866


title: Single nucleus Hi-C cell P54G13


title: R21869


title: Single-cell RNA-seq 48h


title: Single nucleus Hi-C cell P54G12


title: Single nucleus Hi-C cell P54G11


title: R21864


title: Population Hi-C Dnmt3ab KO 24h replicate 1

value: diploid Dnmt3a and b knock out mESC derived from strain E14

value: targeted knock out of Dnmt3a and Dnmt3b genes


title: Single nucleus Hi-C cell P54F7


title: R21862

value: F


title: Population Hi-C Haploid 24hRexH replicate 1


title: R21863


title: Single nucleus Hi-C cell P46G10


title: R21859


title: Single nucleus Hi-C cell P46D12


title: R21861


title: Single nucleus Hi-C cell P54E14


title: R21860


title: R21858


title: Single nucleus Hi-C cell P46D6


title: Single nucleus Hi-C cell P73F6


title: Single nucleus Hi-C cell P73F8


title: Single nucleus Hi-C cell P45F10


title: R21856


title: R21857


title: Single nucleus Hi-C cell P73F5


title: R21855


title: R21868


title: R21854


title: Single nucleus Hi-C cell P73E8


title: Esophageal squamous cell carcinoma [E28SCC]

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

description: ESCC.integrated.rds

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: Esophagus

tag: disease state

value: Esophageal squamous cell carcinoma

tag: age

value: Male


title: R21852

tag: Sex


title: R21853

tag: dsm-5 aud status


title: Single nucleus Hi-C cell P63H14

value: Yes

value: haploid mESCs derived from strain 129/Ola

value: 24 hr Rex1 Low/formative


title: Esophageal squamous cell carcinoma [E25SCC]

description: ESCC.integrated.rds

value: Female


title: Single nucleus Hi-C cell P63H10


title: Esophageal squamous cell carcinoma [E24SCC]

description: ESCC.integrated.rds


title: Single nucleus Hi-C cell P63H7


title: Single nucleus Hi-C cell P63H9


title: Single nucleus Hi-C cell P63G12


title: R21851

value: DLPFC

tag: agedeath


title: Single nucleus Hi-C cell P64E5


title: Single nucleus Hi-C cell P63E9


title: Esophageal squamous cell carcinoma [E19SCC]

description: ESCC.integrated.rds


title: Single nucleus Hi-C cell P63G10


title: non-malignant esophageal mucosa [E16SCN]

description: ESCC.integrated.rds

value: non-malignant esophageal mucosa


title: Single nucleus Hi-C cell P63E14


title: R21849

value: M

tag: dsm-5 major depression diagnosis

value: Case


title: Esophageal squamous cell carcinoma [E18SCC]

description: ESCC.integrated.rds


title: Single nucleus Hi-C cell P64E11


title: Single nucleus Hi-C cell P72E10

value: 24 hr Rex1 High


title: Single nucleus Hi-C cell P62H13


title: Single nucleus Hi-C cell P62H10


title: R21847

tag: current smoker at death


title: R21850

tag: pmi


title: R21845

value: Control

tag: rin


title: R21844

tag: sample plate


title: Single nucleus Hi-C cell P62G8


title: Esophageal squamous cell carcinoma [E17SCC]

description: ESCC.integrated.rds


title: Esophageal squamous cell carcinoma [E23SCC]

description: ESCC.integrated.rds


title: Single nucleus Hi-C cell P62F11


title: Single nucleus Hi-C cell P62G7


title: Single nucleus Hi-C cell P62E12


title: Single nucleus Hi-C cell P63F8


title: R21843

tag: sample well


title: R21842

tag: brain number


title: Single nucleus Hi-C cell P44F6

value: Naive ES


title: Single nucleus Hi-C cell P44F12


title: R21841

tag: tissue


title: R21840


title: R21835


title: M-73_Drug_FD_6

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

description: CpG sites (txt)

data_processing:
The RNA sequencing reads were initially processed through a series of steps. Firstly, cutadapt v1.18 was used to trim the reads, removing polyA/polyT/polyG sequences longer than 30 base pairs, index primers, and low-quality sequences. Reads shorter than 20 base pairs after trimming were also discarded. The remaining high-quality reads were aligned to the human genome (hg19) using STAR v2.7.3 with the GENCODE annotation (version 19)
Using the same reference and annotation, Gene expression levels were quantified using HTSeq v2.0.3 and converted into fragments per kilobase transcript per million mapped reads (FPKM values)
The DNA raw FASTQ read data was initially processed using Trim Galore v0.6.6 to filter out adapters and low-quality reads. Subsequently, the remaining high-quality reads were aligned to the human reference genome (hg19 version) using Bismark v0.22.3 and Bowtie2 v2.4.1, based on the default configuration for paired-end sequencing
Obtaining the CpG sites for each sample using the bismark_methylation_extractor script included with Bismark
Assembly: hg19
Supplementary files format and content: gene expression matix in text file
Supplementary files format and content: CpG sites in text file

source_name: marrow

growth_protocol: K562 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin. GM12878 cells were cultured in Roswell Park Memorial Institute supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin.

extract_protocol:
The RNAs of cells were released by using hypotonic lysis buffer (0.2% TritonX-100, 0.05% Pluronic F68, 1.25 U/μL RNase Inhibitor) for 10 min while remaining DNAs within nucleu were released by using the nucleus lysate (20 mM Tris, 2 mM EDTA, 20 mM KCl, 0.3% Trinton-X100, 1 mg/ml protease, 0.05% Pluronic F68)
DNA libraries were constructed according to scRRBS, and RNA libraries were constructed according to Smart-seq2

treatment_protocol: K562 cells were cultured in medium supplemented with 300 nM Decitabine for 72 hours.

value: marrow

tag: cell line

value: marrow cancer cells

value: WT

value: decitabine treated


title: new-M-17_Drug_FD_10

description: CpG sites (txt)

tag: cell type


title: M-69_Drug_FD_2

description: CpG sites (txt)

tag: genotype


title: M-71_Drug_FD_4

description: CpG sites (txt)

tag: treatment


title: M-74_Drug_FD_7

description: CpG sites (txt)


title: new-M-18_Drug_FD_11

description: CpG sites (txt)


title: new-M-14_Drug_FD_8

description: CpG sites (txt)


title: M-72_Drug_FD_5

description: CpG sites (txt)


title: new-M-16_Drug_FD_9

description: CpG sites (txt)


title: R21833


title: M-68_Drug_FD_1

description: CpG sites (txt)


title: T18_Drug_FR_11

description: expression matrix (txt), sample annotation (txt) and original file (fastq)


title: T17_Drug_FR_10


title: R21832


title: R21831


title: Single nucleus Hi-C cell P44H4


title: T14_Drug_FR_8


title: scMT74_Drug_FR_7


title: scMT73_Drug_FR_6


title: R21830

value: F


title: R21839


title: scMT72_Drug_FR_5


title: scMT71_Drug_FR_4


title: R21837


title: M-70_Drug_FD_3

description: CpG sites (txt)


title: R21829


title: scMT70_Drug_FR_3


title: scMT69_Drug_FR_2


title: R21828


title: R21824


title: DMF-192_WD_6

description: CpG sites (txt)

source_name: lymph

value: lymph

value: Human B lymphocytes


title: DMF-198_WD_8

description: CpG sites (txt)


title: DMF-196_WD_7

description: CpG sites (txt)


title: scMT68_Drug_FR_1


title: M-3_WD_10

description: CpG sites (txt)


title: DMF-130_WD_4

description: CpG sites (txt)


title: DMF-200_WD_9

description: CpG sites (txt)


title: R21827


title: T16_Drug_FR_9


title: DMF-131_WD_5

description: CpG sites (txt)


title: DMF-129_WD_3

description: CpG sites (txt)


title: R21822


title: R21823


title: R21821


title: new-M-13_FD_14

description: CpG sites (txt)


title: DMF-128_WD_2

description: CpG sites (txt)


title: Wild type  F. nucleatum

city: Ithaca

first: Joshua

last: Jones

address: 289 Kimball Hall

institute: Cornell University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: intestines (small intestine and colon)

extract_protocol:
This protocol was adapted from Haber et al 2017. To generated single-cell suspensions, ApcMin/+ and wild type mice were euthanized at 11 weeks of age, colons and small intestines were excised, rinsed with ice cold sterile 1X Ca2+ and Mg2+ free PBS (Gibco, 14190144) and flushed of fecal contents using a blunt 1.5 inch 22G needle filled with ice cold sterile 1X Ca2+ and Mg2+ free PBS (Gibco, 14190144). The tissue was opened longitudinally and sliced into small fragments roughly 1 cm in length. The tissue was incubated in RPMI supplemented with L-glutamine (Corning, 45000-396), 1 mM EDTA (Neta Scientific, QB-A611-E177-10), and 10% FBS (Avantor, 97068-085) for 90 minutes, shaking every 30 minutes. The tissue was then incubated at 37°C for 15 minutes and continuously shaken. The supernatant was passed through a 100 m cell strainer and held on ice until loading the cells on 10X Chromium. The remaining tissue was resuspended in RPMI (Corning, 45000-396) supplemented with 20% FBS (Avantor, 97068-085), 0.1 mg/ml DNase I (Thermo Scientific, 90083), and 0.5 mg/ml collagenase A (Millipore Sigma, 10103586001) and incubated at 37°C on a shaker for 30 minutes. The tissue was then gently mechanically dissociated using a rubber plunger of a syringe. The tissue and the dissociated contents were passed through a 100 m cell strainer. The single cell suspension was then pelleted via centrifugation (400 x g for 10 minutes at 4°C). The cell suspension was resuspended in 1X Ca2+ and Mg2+ free PBS (Gibco, 14190144) containing 0.04% weight/volume BSA (VWR, 97061-420) and combined with earlier collected fraction and placed on ice. Sample viability was determined before loading the cells on 10X Chromium using the Countess II Automated Cell Counter (ThermoFisher). The desired number of transcriptomes from viable cells for each sample was 5000-6000 cells per sample.
Libraries targeting 5000-6000 viable cells per sample (for colon and small intestine tissues) were generated using a 10X Genomics Chromium Controller and the Chromium Next GEM Single Cell 3' Kit v3.1 . Per manufacturer description, briefly, cells were separated into GEMs along with beads coated in oligos that capture mRNAs using a poly-dT sequences. This was followed by cell lysis and barcoded reverse transcription of mRNA, followed by amplification, enzymatic fragmentation, and 5′ adaptor and sample index attachment. The libraries were sequenced using an Illumina NextSeq 2000 run with the 100 bp P2 kit.

value: intestines (small intestine and colon)

value: Wild type

value: Intestinal

tag: strain

value: 6 weeks old

value: F. nucleatum, oral gavage


title: Wild type  enterotoxigenic B. fragilis

description: 10x Genomics

tag: age

value: Enterotoxigenic B. fragilis, oral gavage


title: Wild type  PBS

description: 10x Genomics

value: Phosphate buffered saline, oral gavage


title: DMF-127_WD_1

description: CpG sites (txt)


title: R21820

value: DLPFC

tag: Sex

value: M

value: Case


title: new-M-12_FD_13

description: CpG sites (txt)


title: new-M-10_FD_11

description: CpG sites (txt)


title: new-M-11_FD_12

description: CpG sites (txt)


title: RM-40_FD_10

description: CpG sites (txt)


title: R21818

tag: dsm-5 aud status


title: R21816

tag: agedeath

value: Control


title: ApcMin/+  PBS

description: 10x Genomics

value: ApcMin/+


title: R21815

tag: dsm-5 major depression diagnosis


title: RM-25_FD_6

description: CpG sites (txt)

value: WT


title: ApcMin/+  F. nucleatum

description: 10x Genomics


title: RM-29_FD_8

description: CpG sites (txt)


title: KM1_FD_5

description: CpG sites (txt)

value: marrow

value: marrow cancer cells


title: RM-16_FD_4

description: CpG sites (txt)


title: RM-14_FD_3

description: CpG sites (txt)


title: RM-28_FD_7

description: CpG sites (txt)

value: lymph


title: RM-33_FD_9

description: CpG sites (txt)

value: Human B lymphocytes


title: R21814

tag: current smoker at death


title: RM-13_FD_2

description: CpG sites (txt)


title: R21811

value: F

tag: pmi


title: RM-3_FD_1

description: CpG sites (txt)


title: R21809

tag: rin


title: RNA37_WR_6


title: R21813

tag: sample plate


title: ApcMin/+  enterotoxigenic B. fragilis

description: 10x Genomics

value: intestines (small intestine and colon)


title: RNA36_WR_5


title: RNA35_WR_4


title: R21808

tag: sample well


title: DTT miRNA (D)

city: zhengzhou

last: Yu

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

description: treatment

data_processing:
The raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: Excel include transcript per million (TPM) values for each Sample

organism: Triticum aestivum

source_name: leaves

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). And then we performed the single-end sequencing (50bp) on an Illumina Hiseq2500 (Illumina, San Diego, USA) at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

tag: time

value: 2 days' treatment

value: wheat seedlings


title: DTT+TUDCA miRNA (T)

description: co-treatment


title: RNA20_WR_3

tag: tissue


title: control miRNA (C)

description: control


title: S16_WR_2

tag: cell line


title: S15_WR_1

tag: cell type


title: R21806

tag: brain number


title: DTT+TUDCA degradome (T)

description: co-treatment

data_processing:
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina Hiseq 2500 following vendor’s instruction for running the instrument.
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module.
A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: excel,expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 20 ug of total RNA were used to prepare Degradome library. The method with some modification. (1) Approximately 150 ng of poly(A)+ RNA was used as input RNA and annealing with Biotinylated Random Primers. (2) Strapavidin capture of RNA fragments through Biotinylated Random Primers. (3)5’ adaptor ligation to to only those RNAs containing 5’-monophosphates. (4) Reverse transcription and PCR (5) Libraries were sequenced using the 5’ adapter only, resulting in the sequencing of the first 36 nucleotides of the inserts that represented the 5’ ends of the original RNAs. And then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
Degradome-Seq


title: R21805


title: new-T-13_FR_14

tag: genotype

tag: treatment


title: new-T-12_FR_13


title: DTT degradome (D)

description: treatment

tag: age


title: R21800

tag: Sex


title: scMT33_FR_9


title: scMT40_FR_10


title: new-T-11_FR_12


title: R21799

tag: dsm-5 aud status


title: control degradome (C)

description: control


title: scMT28_FR_7


title: R21798

tag: agedeath


title: scMT25_FR_6


title: scMT29_FR_8


title: KR1_FR_5


title: R21796

tag: dsm-5 major depression diagnosis


title: HiC_H526_sgNONT

city: Chicago

first: Lu

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Hi-C

data_processing:
Hi-C fastq files were first trimmed by trim galore
Trimmed Hi-C fastq files were mapped to hg19 with bwa by runHiC (v0.8.6)
HiC matrices were generated using Pairtools
Assembly: hg19
Supplementary files format and content: hic format of Hi-C 2D contact map, can be visualized using Juicebox

growth_protocol: The SCLC cell lines NCI-H526 was obtained from ATCC, and were maintained with ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma).

extract_protocol:
Hi-C experiments were performed following the Arima manufacture’s protocol. Briefly, chromatin extracted from crosslinked cells was digested with restriction enzymes, followed by biotin labeling, proximity ligation and crosslink reversal. Chromatin was then sheared by sonication and sized selected. The biotin labeled DNA was then enriched and pulled down with streptavidin beads
Hi-C libraries were performed following the protocol for KAPA HyperPrep kit.

value: small cell lung cancer

value: wild type

value: sgRNA nontargeting


title: HiC_H526_sgPOU2AF2-2

description: Hi-C

value: sgPOU2AF2 #2


title: scMT16_FR_4


title: HiC_H526_sgPOU2AF2-1

description: Hi-C

value: sgPOU2AF2 #1


title: scMT14_FR_3


title: scMT13_FR_2


title: R21795

value: DLPFC

value: M

tag: current smoker at death


title: shNC IP

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

data_processing:
Raw reads were trimmed by Trim Ggalore (version 0.6.7) with the parameter ‘--paired’ and were aligned to the human genome (GRCh38) using HISAT2 (version 2.2.1) with default parameters. Unmapped and multi-mapped reads were filtered out using samtools. Counts for annotated genes were generated using featureCounts (version 2.0.1) with the GENCODE V35 annotation file.  The raw counts were converted to TPM by using in house script and differential analysis was performed. exomePeak2 was used for m6A peak calling
Assembly: GRCh38
Supplementary files format and content: narrowPeak

source_name: U-251 MG cells

growth_protocol: U-251 MG cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM), 10% fetal bovine serum, 1× penicillin/streptomycin, 1×Myco-Blue Mycoplasma Detector. Cells were maintained at 37°C in a 5% CO2 atmosphere

extract_protocol:
Total RNAs were extracted utilizing RNA-easy Isolation Reagent (Vazyme, China) and treated with DNase I (Roche, Switzerland), which were then fragmented into 100-150 nt fragments with RNA Fragmentation Reagent (Invitrogen, USA).
The meRIP-seq libraries were used the SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara, Japan). 10 ng of fragmented RNA from each sample was used as starting material for Input and IP samples. Amplification of libraries were performed with 14 cycles on the thermocycler. The samples were sequenced with paired-end on Illumina NovaSeq 6000.

value: U-251 MG cells


title: RNA3_FR_1

value: WT


title: shNC Input


title: new-T-10_FR_11


title: R21794

value: Control

tag: pmi


title: shTRA2A Input


title: R21793

value: Case

tag: rin