title: day 0 - replicate 3 AS-369182-LR-45374

description: day 0 - replicate 3


title: day 0 - replicate 3 AS-369178-LR-45374

status: Public on Oct 02 2023

type: SRA

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

country: Germany

institute: German Cancer Research Center

description: day 0 - replicate 3

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: count matrices - CSV file includes raw counts for each sample
Supplementary files format and content: annotation sheets - CSV file inculding metadata for respective count matrix

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Single cells were sorted directly into 96 well-plates containing 1 µl of lysis buffer per well, centrifuged and snap frozen in liquid nitrogen.
ScRNAseq libraries of tumour cell subpopulations and endothelial cells were constructed using a modified SMART-Seq2 protocol

tag: tissue

value: lung

tag: cell type

value: endothelial cells

tag: genotype

value: WT

tag: treatment

value: uninjected control animals


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title: ChIP_IP Cnd-GFP mit1 replicate 6

city: Lyon

first: Pascal

last: BERNARD

address: 46 allée d'Italie

department: LBMC

country: France

institute: CNRS

description: cnd2 tagged with GFP

library_source: genomic

data_processing:
Process fastq file with fastp (version 0.20.1)
Concatenate the fission yeast genome and the budding yeast (calibration) genome and prefix every chromosomes in the calibration genome with the string calib
Map fastq files on the concatenated genome with bowtie2 (versio 2.3.4.1).
Sort and index bam files with samtools (version 1.11)
Split bam files into bam of reads mapping exclusively on the fission yeast genome and bam of reads mapping exclusively on the calibration genome
Remove duplicated reads with picard (version 2.18.11).
Bam files are converted to bigwig format and and bedgraph format using deeptools (version 3.5.1)
Read numbers in IP samples were normalized according to the internal calibration signal provided by budding yeast SMC3-GFP, using the method of Hu et al. [Hu, B., Petela, N., Kurze, A., Chan, K.-L., Chapard, C., and Nasmyth, K. (2015). Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res. 43, e132.].
To analyze the coverage information at repetitive regions of the genome, we calculated the IP/WCE ratio for each base, as described in the git repository https://gitbio.ens-lyon.fr/LBMC/Bernard/condensin_cal_ChIPseq.git
Assembly: fission yeast genome version ASM294v2 extented with TEL2R DNA sequence.
Supplementary files format and content: ip.bw files are normalized IPs; wce.bw files are normalized Total (Input); IP.OR.bw files are base per base ratios of ip.bw/wce.bw

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: fission yeast mit1 delete cells

growth_protocol: cells exponentailly growing in synthetic PMG medium at 30°C were arrested in metaphase by depletion of the Slp1 protein (APC co-activator) for 2hours, shifted at 36°C for 1 hour, fixed with formaldehyde 1% and processed for calibrated ChIP-seq using budding yeast cells expressing SMC3-GFP for internal calibration

extract_protocol: ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: Fission yeast cells mixed with budding yeast cells (SMC3-GFP) at a ratio of 5:1

value: mit1 null mutant

tag: antibody

value: Iped with anti-GFP antibody


title: ChIP_Input Cnd-GFP WT replicate 6

description: cnd2 tagged with GFP

source_name: fission yeast WT cells

value: Wild-Type

value: Total fraction prior to IP


title: day 0 - replicate 1 AS-368127-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP WT replicate 6

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368131-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP mit1 replicate 5

description: cnd2 tagged with GFP


title: ChIP_Input Cnd-GFP mit1 replicate 5

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368129-LR-45389

description: day 0 - replicate 1


title: ChIP_Input Cnd-GFP WT replicate 5

description: cnd2 tagged with GFP


title: ChIP_IP Cnd-GFP WT replicate 5

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368123-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368125-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP cut14-208 replicate 4

description: cnd2 tagged with GFP

source_name: fission yeast cut14-208mutant cells

value: condensin cut14-208 mutant


title: ChIP_Input Cnd-GFP cut14-208 replicate 4

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368119-LR-45389

description: day 0 - replicate 1


title: ChIP_Input Cnd-GFP WT replicate 4

description: cnd2 tagged with GFP


title: ChIP_Input Cnd-GFP mit1 replicate 6

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368117-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368115-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP WT replicate 4

description: cnd2 tagged with GFP


title: ChIP_Input Cnd-GFP cut14-208 replicate 3

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368113-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368111-LR-45389

description: day 0 - replicate 1


title: ChIP_Input Cnd-GFP WT replicate 3

description: cnd2 tagged with GFP


title: ChIP_IP Cnd-GFP cut14-208 replicate 3

description: cnd2 tagged with GFP


title: day 0 - replicate 1 AS-368109-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368105-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP WT replicate 3

description: cnd2 tagged with GFP


title: Hi-C cut14-208 replicate 2

description: Treated for Hi-C

data_processing:
Raw data was processed through the hicstuff pipeline http://doi.org/10.5281/zenodo.4066363 3.1 version
Genome_build: fission yeast genome version ASM294v2
Supplementary_files_format_and_content: Hi-C matrices in .txt format. Supplementary files (available on the series record) include information for interpreting data in the Hi-C matrices: info_contigs.txt and fragments_list.txt
GCA_000002945_Saccharomyces_cerevisiae.fasta correspond to a modified version of the ASM294v2 version of fission yeast genome from NCBI, concatenated with budding yeast genome (R64 - sacCer3). Briefly,  the**telomere 2 R*(*Tel2R) sequence from plasmid pNSU70 (Sugawara, NF. Ph.D. thesis. Harvard University, Cambridge, Massachusetts) was aligned  with ASM294v2 using Blast, and nucleotides 4137 to 7223 of pNSU70 were  added to the end of the current sequence of chromosome 2 to create a  TEL2R-extended version of the fission yeast ASM294v2 genome. Next, this  TEL2-R extended version of ASM294v2 was concatenated with budding yeast genome (R64 - sacCer3) to create the files GCA_000002945_Saccharomyces_cerevisiae.fasta and GCA_000002945.bed.

source_name: fission yeast cut14-208 mutant cells

growth_protocol: cells exponentailly growing in synthetic PMG medium at 30°C were shifted at 33°C and arrested in metaphase by depletion of the Slp1 protein (APC co-activator) for 3hours, fixed and processed for Hi-C

extract_protocol:
Hi-C protocol
NextFlex DNA Barcoding & PCR mastermix

tag: tagged protein

value: cnd2 tagged with GFP

tag: chip antibody


title: day 0 - replicate 1 AS-368099-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368121-LR-45389

description: day 0 - replicate 1


title: ChIP_Input Cnd-GFP cut3-477 replicate 2

description: Total fraction prior to IP

data_processing:
Process fastq file with fastp (version 0.20.1)
Concatenate the fission yeast genome and the budding yeast (calibration) genome and prefix every chromosomes in the calibration genome with the string calib
Map fastq files on the concatenated genome with bowtie2 (versio 2.3.4.1).
Sort and index bam files with samtools (version 1.11)
Split bam files into bam of reads mapping exclusively on the fission yeast genome and bam of reads mapping exclusively on the calibration genome
Remove duplicated reads with picard (version 2.18.11).
Bam files are converted to bigwig format and and bedgraph format using deeptools (version 3.5.1)
Read numbers in IP samples were normalized according to the internal calibration signal provided by budding yeast SMC3-GFP, using the method of Hu et al. [Hu, B., Petela, N., Kurze, A., Chan, K.-L., Chapard, C., and Nasmyth, K. (2015). Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res. 43, e132.].
To analyze the coverage information at repetitive regions of the genome, we calculated the IP/WCE ratio for each base, as described in the git repository https://gitbio.ens-lyon.fr/LBMC/Bernard/condensin_cal_ChIPseq.git
Genome_build: fission yeast genome version ASM294v2 extented with TEL2R DNA sequence.
GCA_000002945_Saccharomyces_cerevisiae.fasta correspond to a modified version of the ASM294v2 version of fission yeast genome from NCBI, concatenated with budding yeast genome (R64 - sacCer3). Briefly,  the**telomere 2 R*(*Tel2R) sequence from plasmid pNSU70 (Sugawara, NF. Ph.D. thesis. Harvard University, Cambridge, Massachusetts) was aligned  with ASM294v2 using Blast, and nucleotides 4137 to 7223 of pNSU70 were  added to the end of the current sequence of chromosome 2 to create a  TEL2R-extended version of the fission yeast ASM294v2 genome. Next, this  TEL2-R extended version of ASM294v2 was concatenated with budding yeast genome (R64 - sacCer3) to create the files GCA_000002945_Saccharomyces_cerevisiae.fasta and GCA_000002945.bed.
Supplementary_files_format_and_content: IP_norm.bw files are normalized IPs; T_norm.bw files are normalized Total (Input); ratio_IP_norm.bw files are base per base ratios of IP_norm / T_norm.

source_name: fission yeast cut3-477 mutant cells

growth_protocol: cells exponentially growing in synthetic PMG medium at 30°C were arrested in metaphase by depletion of the Slp1 protein (APC co-activator) for 2hours, shifted at 36°C for 1 hour, fixed with formaldehyde 1% and processed for calibrated ChIP-seq against Fission yeast Cnd2-GFP, using budding yeast cells expressing SMC3-GFP for internal calibration. IP were performed with anti-GFP polyclonal antibody #A111-22 (Invitrogen)

extract_protocol:
ChIP
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: condensin cut3-477 mutant

value: none (input)


title: Hi-C WT replicate 2

description: Treated for Hi-C


title: day 0 - replicate 1 AS-368097-LR-45389

description: day 0 - replicate 1


title: Hi-C cut14-208 replicate 1

description: Treated for Hi-C


title: day 0 - replicate 1 AS-368103-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368107-LR-45389

description: day 0 - replicate 1


title: Hi-C WT replicate 1

description: Treated for Hi-C


title: day 0 - replicate 1 AS-368095-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP cut3-477 replicate 2

description: Iped with anti-GFP antibody

value: anti-GFP


title: day 0 - replicate 1 AS-368093-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP WT replicate 2

description: Iped with anti-GFP antibody


title: day 0 - replicate 1 AS-368091-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368089-LR-45389

description: day 0 - replicate 1


title: ChIP_Input Cnd-GFP WT replicate 2

description: Total fraction prior to IP


title: ChIP_Input Cnd-GFP cut3-477 replicate 1

description: Total fraction prior to IP


title: ChIP_IP Cnd-GFP cut3-477 replicate 1

description: Iped with anti-GFP antibody


title: ChIP_Input Cnd-GFP WT replicate 1

description: Total fraction prior to IP


title: day 0 - replicate 1 AS-368085-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368087-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368101-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368081-LR-45389

description: day 0 - replicate 1


title: VCaP-CR_shFAM3B_4

city: New Orleans

first: Yan

last: Dong

address: 1700 Tulane Ave

country: USA

institute: Tulane University

library_source: transcriptomic

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using bowtie. Gene expression was calculated by using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: VCaP

growth_protocol: C4-2 and VCaP cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
Poly-A selected unstranded RNA-seq libraries of C4-2 cells were constructed by Novogene Co, and Poly-A selected stranded RNA-seq libraries of VCaP tumors were constructed by the BGI.

treatment_protocol:
FAM3B-inducible-expressing C4-2 cells and the control cells were treated with 200 ng/ml doxycycline for 48 hours.
Control-shRNA- or FAM3B-shRNA-expressing VCaP cells were mixed with 50% matrigel and inoculated subcutaneously into male CB17 SCID mice at 6-7 weeks of age. Mice were castrated when tumors reached ~100 mm3. At the termination of the experiment, the mice were sacrificed, and tumors were collected for molecular analysis.

tag: cell line

value: VCaP

value: xenograft tumors

value: FAM3B knockdown

value: androgen deprivation

tag: time

value: 3 weeks


title: day 0 - replicate 1 AS-368083-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells


title: day 0 - replicate 1 AS-368079-LR-45389

description: day 0 - replicate 1

value: WT

value: uninjected control animals


title: day 0 - replicate 1 AS-368077-LR-45389

description: day 0 - replicate 1


title: VCaP-CR_shFAM3B_1


title: VCaP-CR_shFAM3B_2


title: day 0 - replicate 1 AS-368071-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368075-LR-45389

description: day 0 - replicate 1


title: VCaP-CR_shCtrl_4


title: VCaP-CR_shCtrl_3


title: day 0 - replicate 1 AS-368069-LR-45389

description: day 0 - replicate 1


title: VCaP-CR_shCtrl_1


title: day 0 - replicate 1 AS-368073-LR-45389

description: day 0 - replicate 1


title: VCaP-CR_shCtrl_2


title: day 0 - replicate 1 AS-368067-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368063-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368065-LR-45389

description: day 0 - replicate 1


title: 3d_4

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Raw reads were trimmed by tool Trimmomatic to remove low-quality reads
Reads were aligned to human reference genome by STAR aligner, and quantified by STAR --quant  Mode GeneCounts function
Assembly: mm10
Supplementary files format and content: TXT read count

source_name: kidney

extract_protocol:
Total RNA was extracted using the TRIzol RNA isolation system.
Follow Illumina TruSeq kit

value: kidney

tag: strain

tag: gender

value: Male

tag: age

value: 8 weeks


title: 3d_3


title: 3d_2


title: day 0 - replicate 1 AS-368061-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368059-LR-45389

description: day 0 - replicate 1


title: ChIP_IP Cnd-GFP WT replicate 1

description: Iped with anti-GFP antibody

value: Wild-Type


title: VCaP-CR_shFAM3B_3


title: 3d_1


title: day 0 - replicate 1 AS-368057-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368055-LR-45389

description: day 0 - replicate 1


title: 1d_5


title: 1d_3


title: 1d_4


title: day 0 - replicate 1 AS-368053-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368047-LR-45389

description: day 0 - replicate 1


title: 1d_1


title: 0d_3


title: day 0 - replicate 1 AS-368043-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368041-LR-45389

description: day 0 - replicate 1


title: 3d_5


title: 0d_4


title: day 0 - replicate 1 AS-368045-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368049-LR-45389

description: day 0 - replicate 1


title: 1d_2


title: day 0 - replicate 1 AS-368039-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368035-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368033-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368031-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368037-LR-45389

description: day 0 - replicate 1


title: Wildtype RNA-seq at 37C replicate 2

city: New York

first: Jitong

last: Cai

state: NY

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

description: wildtype strain BY4741 in 37C YPD as control

data_processing:
For applications requiring similar numbers of reads per sample, downsampling was performed using seqtk v1.3. Samples were first processed using Trimmomatic v0.39 and FastQC v0.11.4.
Processed reads were aligned to the S288C transcriptome and a custom synIX transcriptome (in which chromosome IX transcripts were replaced with their synthetic versions) using Kallisto v0.46.0 and STAR v2.5.2a.
STAR-aligned results were further processed using SAMtools v1.9 and BEDtools v2.26.0, and visualized in IGV v2.7.2.
Kallisto pseudoalignment data was further processed in RStudio version 1.3.1093 using the sleuth v0.30.0 and ggplot2 v3.3.5 packages.
Assembly: S288C
Supplementary files format and content: comma-delimited txt file contains a list of differential expression genes and related statistics
Supplementary files format and content: tab-delimited txt file contains the raw read count for each gene

organism: Saccharomyces cerevisiae BY4741

growth_protocol: A single yeast colony was inoculated in 5 mL of YPD liquid medium at 30C overnight with rotation. Overnight yeast culture was diluted to A600=0.15-0.2 into 6 mL of fresh YPD liquid medium and grown at 30C or 37C with rotation until A600 reached 0.8-1.0.

extract_protocol:
Yeast cells were harvested from 4 mL of culture, and total RNA was extracted using the RNeasy extraction kit (QIAGEN, 74106) according to the manufacturer’s instructions. RNA was quantified using the Qubit BR RNA Assay Kit (Thermo Fisher Scientific, Q10210).
1 ug total RNA was used as input for the QIAseq Stranded Total RNA Library Kit (QIAGEN, 180745) plus QIAseq FastSelect -rRNA Yeast Kit (QIAGEN, 334217).


title: Wildtype RNA-seq at 37C replicate 1


title: SynIX RNA-seq at 37C replicate 3

description: SynIX strain yLHM1601 cultured in 37C YPD

value: SynIX


title: Wildtype RNA-seq at 37C replicate 3


title: day 0 - replicate 1 AS-368029-LR-45389

description: day 0 - replicate 1


title: SynIX RNA-seq at 37C replicate 2


title: day 0 - replicate 1 AS-368027-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368051-LR-45389

description: day 0 - replicate 1


title: 0d_2


title: 0d_1


title: Wildtype RNA-seq at 30C replicate 2

description: wildtype strain BY4741 in 30C YPD as control


title: day 0 - replicate 1 AS-368023-LR-45389

description: day 0 - replicate 1


title: Wildtype RNA-seq at 30C replicate 3


title: day 0 - replicate 1 AS-368025-LR-45389

description: day 0 - replicate 1


title: Wildtype RNA-seq at 30C replicate 1


title: SynIX RNA-seq at 37C replicate 1


title: day 0 - replicate 1 AS-368021-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-368019-LR-45389

description: day 0 - replicate 1


title: SynIX RNA-seq at 30C replicate 2

description: SynIX strain yLHM1601 cultured in 30C YPD


title: SynIX RNA-seq at 30C replicate 3


title: day 0 - replicate 1 AS-368017-LR-45389

description: day 0 - replicate 1


title: Small intestinal tumor No.2-2-32

type: genomic

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: Research Institutes for Quantum Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).  The numerical data were analyzed with Agilent Genomic Workbench software. For normalization, centralization was applied, with a threshold value of 6.0 and a Bin Size of 10.

source_name: Small intestinal tumors in mice irradiated with 2 Gy of gamma rays

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 2°C) and humidity (55 ± 10%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet and water ad libitum.

extract_protocol: Genomic DNA of small intestinal tumors and normal small intestine were extarcted by AllPrep DNA/RNA Micro Kit.

treatment_protocol: Mice were left untreated or were subjected to whole-body irradiated with gamma-rays (2 Gy)  at 2 weeks of age.

value: small intestinal tumor

value: B6/B6-Chr18MSM-F1 ApcMin/+

source_name: Normal small intestine

value: Small intestine

value: pooled male and female


title: Small intestinal tumor No.2-2-29


title: SynIX RNA-seq at 30C replicate 1


title: Small intestinal tumor No.0-2-15

source_name: Small intestinal tumors in non-irradiated mice


title: Small intestinal tumor No.2-2-19


title: Small intestinal tumor No.2-2-56


title: day 0 - replicate 1 AS-368015-LR-45389

description: day 0 - replicate 1


title: OA-500 µM treated day 25 OS-HLOs, replicate 2, scRNAseq

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

description:
SM-L3XWJ
10x Genomics

data_processing:
Raw bcl files were converted to fastq by the command bcl2fastq --use-bases-mask Y26,I8,Y98. Demultiplexing, barcoded processing, gene counting, aggregation and alignment to the GRCh38 genome was performed with the cellranger software version 3.0.2. Downstream analysis was performed in python (version => 3.6) with scanpy version => 1.7.2.
Assembly: GRCh38 (human)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Human liver organoid (HLO)

growth_protocol: HLOs were generated from hPSCs. ULA-HLOs were grown for 21 or 34 days. OS-HLOs were cultured for 20 days before undergoing 5 days of treatment.

extract_protocol:
Freshly collected human liver organoids were washed 1X with warm DPBS(-/-) and briefly dissociated by incubation with 0.05-0.25% Trypsin-EDTA for 10 minutes at 37°C. Day 34 ULA- and day 25 OS-HLOs underwent an additional DBPS (-/-) wash and 10 minutes of trypsinization to allow complete digestion. For each replicate, full single cell dissociation was confirmed manually by light microscopy. After a final DPBS(-/-) wash, organoids were resuspended in DPBS(-/-), counted after with the TC20™ Automated Cell Counter (Trypan Blue) and transferred on ice for library preparation.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: OS-HLOs were treated for 5 days with TGF-β1 (10 ng/ml) or PA (500 µM).

value: Human liver organoid (HLO)

value: W01, WiCell

value: hPSC-derived HLOs

value: Wild-type

value: OA 500 uM

value: day 25


title: OA-500 µM treated day 25 OS-HLOs, replicate 1, scRNAseq

description:
SM-L3XWI
10x Genomics


title: Control-for-OA day 25 OS-HLOs, replicate 2, scRNAseq

description:
SM-L3XWH
10x Genomics

value: Control-OA


title: day 0 - replicate 1 AS-368013-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: WT

value: uninjected control animals


title: Small intestinal tumor No.2-2-26

value: Male


title: day 0 - replicate 1 AS-368011-LR-45389

description: day 0 - replicate 1


title: phoR KO 4.5-REPLICATE 3

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

country: India

institute: CSIR-IMTECH

data_processing:
Basecalling, demultiplication and adaptor trimming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (Mycobacterium tuberculosis H37Rv accession number NC_000962.3) using Hisat2.
Differential gene expression analysis of samples with respect to control was performed using Cuffdiff program (v2.2.1).
Assembly: NC_000962.3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Mycobacterium tuberculosis

source_name: bacteria

growth_protocol: M. tuberculosis H37Rv strains were grown at 37°C in Middlebrook 7H9 broth (Difco) containing 0.2% glycerol, 0.05% Tween-80 and 10% Middlebrook ADC (albumin-dextrose-catalase).

extract_protocol:
RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown (in the indicated pH) to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen).
Total RNA was isolated using Direct-zol RNA MiniPrep kit(Zymo Research Corporation),thepurity of isolated RNA was determined using the NanoDrop (ThermoScientific), quantified using Qubit (Invitrogen), and RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies).Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India.Briefly,The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was carried out using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated.Thereads that passed quality control were mapped onto the reference genome ofM. tuberculosisH37Rv usingHisat2(version-2.0.5).The abundance of transcripts in individual samples was estimated usingCufflinks (v2.2.1).

treatment_protocol: Cultures were grown till mid log phase and then divided into two halves. One part was exposed to acidic stress (pH 4.5) and other one to normal conditions (pH 7.0) for 2 hours. RNA was isolated and processed for RNA sequencing.

value: bacteria


title: Small intestinal tumor No.2-2-39

value: small intestinal tumor


title: phoR KO 4.5-REPLICATE 4


title: Small intestinal tumor No.2-2-5

value: B6/B6-Chr18MSM-F1 ApcMin/+


title: Control-for-OA day 25 OS-HLOs, replicate 1, scRNAseq

description:
SM-L3XWG
10x Genomics


title: Small intestinal tumor No.2-2-23

value: Small intestine


title: Small intestinal tumor No.0-2-24

value: pooled male and female


title: Small intestinal tumor No.0-2-4


title: Small intestinal tumor No.2-2-43


title: Small intestinal tumor No.0-1-11

value: Female


title: Day 25 OS-HLOs, replicate 2, scRNAseq

description:
SM-L3XWF
10x Genomics

value: Human liver organoid (HLO)

value: W01, WiCell


title: phoR KO 7.0-REPLICATE 4


title: day 0 - replicate 1 AS-368009-LR-45389

description: day 0 - replicate 1


title: Small intestinal tumor No.0-1-12


title: Small intestinal tumor No.0-1-3


title: Small intestinal tumor No.0-2-12


title: GM, siSTAT5B (Rep 3)

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

description:
Sample from third out of three independent repeat experiments.
20_GM_siSTAT5B

data_processing:
Quality of raw sequences was inspected with FastQC (v0.11.9).
Sequenced reads were trimmed for adaptor sequence using cutadaptor v3.5 with parameters "cutadapt -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o output_file.fastq.gz input_file.fastq.gz".
Trimmed reads were mapped to the Ensembl reference human transcriptome GRCh38.p13 cDNA using kallisto v0.46.2 and were sebseqently quantified as read count at gene level based on the Ensemble GRCh38.104 GTF annotation file.
Genes with an average count < 5 were removed from the analysis.
Assembly: GRCh38.p13
Supplementary files format and content: exp_counts.tsv (tab-delimited text file includes read count values for each sample)

source_name: Monocyte-derived macrophages

growth_protocol:
RPMI + 1% Penicillin/Streptomycin + 10% foetal bovine serum
Differentiation of cells induced by 5 ng/ml recombinant human GM-CSF

extract_protocol:
total RNA was isolated from macrophages using the Micro RNeasy kit (Qiagen) according to the <100,000 cells protocol. RNA quality and integrity were assessed using a TapeStation System (Agilent).
The NEBNext® Poly (A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 2000 System and NextSeq P3 sequencing reagent kit in a single read-mode with a read-length of 72 bp and dual unique index sequences.

treatment_protocol: Viromer + 12.5 nM siRNA final concentration for 24h. Afterwards resting of cells for 24h in RPMI + 1% Penicillin/Streptomycin + 10% foetal bovine serum

value: Monocyte-derived macrophages

value: STAT5B siRNA


title: phoR KO 7.0-REPLICATE 3


title: Day 25 OS-HLOs, replicate 1, scRNAseq

description:
SM-L3XWE
10x Genomics

value: hPSC-derived HLOs

value: Wild-type

value: day 25


title: GM, siSTAT5B (Rep 2)

description:
Sample from second out of three independent repeat experiments.
19_GM_siSTAT5B


title: day 0 - replicate 1 AS-368007-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells


title: GM, siSTAT5B (Rep 1)

description:
Sample from first out of three independent repeat experiments.
18_GM_siSTAT5B


title: GM, siSTAT5A (Rep 3)

description:
Sample from third out of three independent repeat experiments.
16_GM_siSTAT5A

value: STAT5A siRNA


title: day 0 - replicate 1 AS-368005-LR-45389

description: day 0 - replicate 1

value: WT

value: uninjected control animals


title: KO 3 scRNAseq

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: 10x genomics

data_processing:
Fastq files were generated using the 10X CellRanger v6.0.2 mkfastq command
Alignment and gene matrix quantification was performed using the 10X CellRanger v6.0.2 count feature using the mm10 reference
Assembly: mm10
Supplementary files format and content: matrix, features and barcodes datafiles created by 10X CellRanger count; tab separated

source_name: brain -cortex

extract_protocol:
Timed-pregnant females were sacrificed to collect embryos (E16.5). Brains were collected from the embryos (n=3 for WT and KO, n=4 for Het), then the cortex was carefully removed using a stereo microscope from each embryo and placed in a 15 ml tube containing Hibernate E/B27/GlutaMax (HEB) media (BrainBits). Tissue pieces from the cortex were then incubated in a Papain solution (BrainBits) at 37°C for 20 minutes. Following this, the Papain solution was gently removed and replaced with the HEB media. The tissues were manually disrupted using a polished Pasteur pipette for a maximum of 10 times. After disruption we allowed the tissue debris to settle for 1 minute at room temperature, the supernatant was transferred to a new tube and centrifuged at 200 rcf for 2 minutes to collect the cells. The supernatant was then carefully removed, and the cell pellet was resuspended in 1 ml of pre-warmed neuronal culture medium (NbActiv1). Subsequently the cell suspension was passed through a 30 µM cell strainer (Miltenyi Biotech) and an aliquot was used for counting using the Automated cell counter (Invitrogen) and morphological evaluation. Single cell suspensions containing more than 90% viable cells were used for the generation of single-cell RNA sequencing libraries. Fast genotyping (~1h) was performed with tissue from the rest of the body using Platinum Direct PCR Universal Master Mix
Single-cell RNA-seq libraries were generated using the 10X Genomics platform (Chromium Single Cell 3′ library and Gel Bead Kit v3, PN-1000075) and sequenced on a NovaSeq 6000 system (Illumina) at the Center for Genome Technology at the HIHG. Cells at a concentration of 1200 cell/mL were loaded on the 10X Genomics Chromium platform to isolate ~7,000 cells per sample and create individually barcoded Gel bead-in-Emulsions (GEMs) which were processed using the Chromium Single Cell 3’ Reagent Version 3 Kit. Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA, USA), and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000 targeting 100,000 reads per cell with sequencing parameters: Read1, 28 cycles; Index1, 8 cycles; Read2, 98 cycles.

value: brain -cortex

value: gatad2b KO


title: GM, siSTAT5A (Rep 2)

description:
Sample from second out of three independent repeat experiments.
15_GM_siSTAT5A


title: GM, siCtr (Rep 3)

description:
Sample from third out of three independent repeat experiments.
12_GM_siCtr

value: Control siRNA


title: day 0 - replicate 1 AS-368003-LR-45389

description: day 0 - replicate 1


title: KO 2 scRNAseq

description: 10x genomics


title: GM, siCtr (Rep 2)

description:
Sample from second out of three independent repeat experiments.
10_GM_siCtr


title: day 0 - replicate 1 AS-368001-LR-45389

description: day 0 - replicate 1


title: KO 1 scRNAseq

description: 10x genomics


title: GM, siCtr (Rep 1)

description:
Sample from first out of three independent repeat experiments.
9_GM_siCtr


title: day 0 - replicate 1 AS-367999-LR-45389

description: day 0 - replicate 1


title: Het 3 scRNAseq

description: 10x genomics

value: gatad2b het


title: Day 34 ULA-HLOs, replicate 2, scRNAseq

description: 10x Genomics

data_processing:
Raw bcl files were converted to fastq by the command bcl2fastq --use-bases-mask Y26,I8,Y98. Demultiplexing, barcoded processing, gene counting, aggregation and alignment to the GRCh38 genome was   performed with the cellranger software version 3.0.2 or 6.0.2. Downstream analysis was performed in python (version => 3.6) with scanpy (version => 1.7.2).
Assembly: GRCh38 (human)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Freshly collected human liver organoids were washed 1X with warm DPBS(-/-) and briefly dissociated by incubation with 0.05-0.25% Trypsin-EDTA for 10 minutes at 37°C.   Day 34 ULA- and day 25 OS-HLOs underwent an additional DBPS (-/-) wash and 10 minutes of trypsinization to allow complete digestion. For each replicate, full single cell dissociation was confirmed manually by light microscopy. After a final DPBS(-/-) wash, organoids were resuspended in DPBS(-/-), counted after with the TC20™ Automated Cell Counter (Trypan Blue) and transferred on ice for library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: day 34


title: Control-for-TGFB1 day 25 OS-HLOs, replicate 2, scRNAseq

description: 10x Genomics

value: Human liver organoid (HLO)


title: TGFB1-10ng/ml treated day 25 OS-HLOs, replicate 2, scRNAseq

description: 10x Genomics

value: W01, WiCell

value: TGF-B1 10 ng/ml


title: TGFB1-10ng/ml treated day 25 OS-HLOs, replicate 1, scRNAseq

description: 10x Genomics


title: Day 34 ULA-HLOs, replicate 1, scRNAseq

description: 10x Genomics


title: Het 4 scRNAseq

description: 10x genomics


title: Het 2 scRNAseq

description: 10x genomics


title: day 0 - replicate 1 AS-367995-LR-45389

description: day 0 - replicate 1


title: Control-for-TGFB1 day 25 OS-HLOs, replicate 1, scRNAseq

description: 10x Genomics


title: day 0 - replicate 1 AS-367993-LR-45389

description: day 0 - replicate 1


title: Day 21 ULA-HLOs, replicate 3, scRNAseq

description: 10x Genomics

value: day 21


title: Het 1 scRNAseq

description: 10x genomics


title: Day 21 ULA-HLOs, replicate 2, scRNAseq

description: 10x Genomics

value: hPSC-derived HLOs


title: GM, siSTAT5A (Rep 1)

description:
Sample from first out of three independent repeat experiments.
13_GM_siSTAT5A

value: Monocyte-derived macrophages


title: WT3 scRNAseq

description: 10x genomics

value: gatad2b WT


title: day 0 - replicate 1 AS-367991-LR-45389

description: day 0 - replicate 1

value: lung


title: Day 21 ULA-HLOs, replicate 1, scRNAseq

description: 10x Genomics

value: Wild-type


title: Intravenous (i.v.) rMVA.scIL12 treated tumors, biological replicate 5

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

data_processing:
FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GrCM39/mm39 using STAR aligner with standard parameters for paired-end sequencing
Read count quantification were performed with featureCounts and normalization were accomplished using edgeR pipeline
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tumor-bearing omentum

growth_protocol: 5x10^5 MC38 tumor cells were intraperitoneally injected in C57BL/6 mice. 7 days later, mice were treated as described below.

extract_protocol:
Tumor-bearing omenta were excised 24 hours after treatment. Tumor-bearing omenta were storaged in RNAlater at -80C until further processing.mRNA was isolated using Rneasy Mini Kit (Qiagen) following manufacture's instructions.
Library preparation and sequencing was developed by Unidad de Genómica (NGS) CIMA- Universidad de Navarra. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA.

treatment_protocol: Control groups received 200μL of vehicle control (PBS).Treatment groups were treated intreperitoneally with 5×10^7 TCID50 (200μL diluted in PBS)of the rMVA. empty or rMVA.scIL12 .Anoter group was treated with an intravenous injection (retro-orbirtal) of rMVA.scIL12 (100μL diluted in PBS)

value: tumor-bearing omentum

value: rMVA.scIL12 i.v.


title: day 0 - replicate 1 AS-367989-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: WT

value: uninjected control animals


title: Intravenous (i.v.) rMVA.scIL12 treated tumors, biological replicate 3


title: WT2 scRNAseq

description: 10x genomics

value: brain -cortex


title: day 0 - replicate 1 AS-367987-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367997-LR-45389

description: day 0 - replicate 1


title: Intravenous (i.v.) rMVA.scIL12 treated tumors, biological replicate 2


title: day 0 - replicate 1 AS-367985-LR-45389

description: day 0 - replicate 1


title: WT1 scRNAseq

description: 10x genomics


title: day 0 - replicate 1 AS-367981-LR-45389

description: day 0 - replicate 1


title: Intraperitoneally (i.p.) rMVA.scIL12 treated tumors, biological replicate 5

value: rMVA.scIL12 i.p.


title: day 0 - replicate 1 AS-367983-LR-45389

description: day 0 - replicate 1


title: Intravenous (i.v.) rMVA.scIL12 treated tumors, biological replicate 1


title: Intraperitoneally (i.p.) rMVA.scIL12 treated tumors, biological replicate 3


title: rat hippocampal neuronal culture, S-SCAM KD, biol rep 1

city: Bordeaux

first: Julio

middle: Santos

last: Viotti

address: 146 Rue Léo Saignat

institute: Institute for Interdisciplinary Neuroscience (IINS)

description: ProcessedData_Dresbach_635.xls column name: KD12

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Read alignment was performed using STAR v2.3.0 to the Rattus norvegicus v5 reference genome.
Data were converted and sorted by samtools 1.2 and reads per gene were counted via htseq version 0.6.
Data analysis was performed using R (3.2.1) - differential gene expression was performed using DESeq2 (v1.8.1)
Assembly: rn5
Supplementary files format and content: xls spreadsheet containing number of reads for each transcript (row) and every sample (column)

organism: Rattus norvegicus

source_name: hippocampal neuronal primary culture

growth_protocol: Rat hippocampi were dissected in HBSS and digested with trypsin for 20 min at 37°C. Hippocampi were triturated, counted and plated in DMEM medium with the addition of B-27 supplement, glutamine and penicillin/streptomycin. After 4 hours medium was changed to Neurobasal medium with the addition of B-27 supplement, glutamine and penicillin/streptomycin (Invitrogen). High-density cultures (40,000 neurons/well) were plated on poly-L-lysine coated 13-mm glass coverslips in 24-well plates

extract_protocol:
RNA was isolated using the TRIzol® Reagent (Life Technologies) according to manufacturer instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation for RNA-Seq was performed using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Cat. N°RS-122-2002) starting from 3000 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (average 350 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; ~30-40 million reads per sample).

treatment_protocol: At DIV2 hippocampal neurons were infected with lentiviruses delivering KD shRNAs directed against S-SCAM/MAGI2. As control an empty shRNA vector was used.

value: Hippocampal neurons

value: S-SCAM KD

value: DIV 9


title: Intraperitoneally (i.p.) rMVA.scIL12 treated tumors, biological replicate 4


title: rat hippocampal neuronal culture, S-SCAM KD, biol rep 3

description: ProcessedData_Dresbach_635.xls column name: KD5


title: day 0 - replicate 1 AS-367977-LR-45389

description: day 0 - replicate 1

source_name: lung


title: Multiplexed cells, scRNA Seq

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

institute: Saarland University

description: BD Rhapsody

data_processing:
Raw data were processed, demultiplexed and mapped by the BD Rhapsody™ WTA Analysis Pipeline on the sevenbridges platform.
H3_SampleTag01_mm_FB1_RSEC_MolsPerCell.csv = FB1, Fibroblast culture
H3_SampleTag04_mm_Ep2_RSEC_MolsPerCell.csv = Ep2, Epithelial cell culture
H3_SampleTag09_mm_Ep5_RSEC_MolsPerCell.csv = Ep5, Epithelial cells from co-culture epithelial cells and fibroblasts
H3_SampleTag10_mm_FB5_310ul_RSEC_MolsPerCell.csv = FB5, Fibroblasts from co-culture epithelial cell and fibroblasts
Assembly: GRCm38-PhiX-gencodevM19-20181206
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Cells from air liquid interface cultures were collected by TrypLE detachment, washed in PBS w/o Mg_Ca, resuspended in BD Rhypsody Buffer
BD Rhapsody Library construction, according to manufacturer's instructions

value: Lung

value: 8-10 weeks

value: untreated


title: rat hippocampal neuronal culture, S-SCAM KD, biol rep 2

description: ProcessedData_Dresbach_635.xls column name: KD29


title: day 0 - replicate 1 AS-367979-LR-45389

description: day 0 - replicate 1


title: rMVA.empty (MVA-BN) treated tumors, biological replicate 4

value: rMVA.empty i.p.


title: Intraperitoneally (i.p.) rMVA.scIL12 treated tumors, biological replicate 2


title: rMVA.empty (MVA-BN) treated tumors, biological replicate 5


title: day 0 - replicate 1 AS-367975-LR-45389

description: day 0 - replicate 1


title: Intraperitoneally (i.p.) rMVA.scIL12 treated tumors, biological replicate 1


title: Intravenous (i.v.) rMVA.scIL12 treated tumors, biological replicate 4


title: rat hippocampal neuronal culture, Control, biol rep 2

description: ProcessedData_Dresbach_635.xls column name: Co29


title: rMVA.empty (MVA-BN) treated tumors, biological replicate 3


title: day 0 - replicate 1 AS-367973-LR-45389

description: day 0 - replicate 1


title: rat hippocampal neuronal culture, Control, biol rep 1

description: ProcessedData_Dresbach_635.xls column name: Co12


title: rMVA.empty (MVA-BN) treated tumors, biological replicate 2


title: day 0 - replicate 1 AS-367971-LR-45389

description: day 0 - replicate 1


title: MIM MG Sample #6 (37MIM)

city: San Francisco

first: Stephanie

middle: L.

last: Gaw

state: CA

address: 513 Parnassus Avenue, Health Sciences East 1622

department: Obstetrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

data_processing:
FASTQ files were aligned to the human reference genome (GRCh37/hg19) using BWA (Burrows-Wheeler Alignment tool).
Aligned BAM files were processed using htseqcount to obtain counts-per-million (CPM) values.
Genes with CPM values > 0.5 in at least two samples were considered expressed above background.
Data were further transformed using VOOM (93) and differentially expressed transcripts were identified using LIMMA.
Genes missing a HGNC symbol were excluded in downstream analyses.
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each sample and statistical parameters based on HBC vs MIM comparison
Supplementary files format and content: csv file includes statistical parameters based on primigravida vs multigravida comparison

source_name: placenta

extract_protocol:
RNA was extracted from isolated MIMs and HBCs using a RNeasy Micro Kit (Qiagen) following the standard manufacturer’s protocol. RNA quality was assessed using an Agilent 2100 BioAnalyzer (RIN > 7).
cDNA and library construction were conducted using 1 µg RNA per sample and sequenced on an Illumina HiSeq 2500 to obtain ~30 million reads per sample.

value: placenta

value: maternal intervillous monocyte

tag: maternal gravidity

value: primigravida


title: rMVA.empty (MVA-BN) treated tumors, biological replicate 1

value: tumor-bearing omentum


title: day 0 - replicate 1 AS-367969-LR-45389

description: day 0 - replicate 1

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: count matrices - CSV file includes raw counts for each sample
Supplementary files format and content: annotation sheets - CSV file inculding metadata for respective count matrix

extract_protocol:
Single cells were sorted directly into 96 well-plates containing 1 µl of lysis buffer per well, centrifuged and snap frozen in liquid nitrogen.
ScRNAseq libraries of tumour cell subpopulations and endothelial cells were constructed using a modified SMART-Seq2 protocol

value: lung


title: HBC MG Sample #6 (37HBC)

value: fetal Hofbauer cell


title: day 0 - replicate 1 AS-367967-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: WT


title: day 0 - replicate 1 AS-367965-LR-45389

description: day 0 - replicate 1

value: uninjected control animals


title: Vehicle (PBS) control treated tumors, biological replicate 5

value: Control (PBS) i.p.


title: HBC MG Sample #5 (33HBC)

value: multigravida


title: rat hippocampal neuronal culture, Control, biol rep 3

description: ProcessedData_Dresbach_635.xls column name: Co5

value: Hippocampal neurons


title: day 0 - replicate 1 AS-367961-LR-45389

description: day 0 - replicate 1


title: Omentum naïve, replicate 3

source_name: Omentum naive

value: Omentum naive

value: not applicable


title: MIM MG Sample #3 (30MIM)


title: MIM PG Sample #4 (31MIM)


title: day 0 - replicate 1 AS-367959-LR-45389

description: day 0 - replicate 1


title: Vehicle (PBS) control treated tumors, biological replicate 2


title: Vehicle (PBS) control treated tumors, biological replicate 3


title: Omentum naïve, replicate 2


title: HBC PG Sample #4 (31HBC)


title: Vehicle (PBS) control treated tumors, biological replicate 1


title: MIM PG Sample #2 (26MIM)


title: day 0 - replicate 1 AS-367955-LR-45389

description: day 0 - replicate 1


title: HBC MG Sample #3 (30HBC)


title: day 0 - replicate 1 AS-367953-LR-45389

description: day 0 - replicate 1


title: Omentum naïve, replicate 1


title: HBC PG Sample #2 (26HBC)


title: MIM MG Sample #5 (33MIM)


title: MIM MG Sample #1 (23MIM)


title: Vehicle (PBS) control treated tumors, biological replicate 4


title: Hela, no sodium fluoroacetate treatment, rep2

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

country: China

institute: Wuhan University

data_processing:
Raw reads were processed to remove adapters and low-quality bases with Trim Galore (v0.6.7).
Reads were first mapped to human rRNA sequences with bowtie2 (v2.2.5). Coverage near 18S modified sites were analyzed with deeptools bamCompare (v3.5.1).
Unmapped reads were next mapped to human genome (hg38) with STAR (v2.7.0d).
Peak calling and differential analysis were processed with exomepeak (v2.16.0).
Assembly: hg38
Supplementary files format and content: bigwig, normalized align result

source_name: Hela

growth_protocol: HeLa, HEK293T and MDA-MB-231 cells were maintained at 37 ℃ in DMEM (Procell, PM150210) medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under 5% CO2. K562 and K562/ADR cells were maintained at 37 ℃ in RPMI-1640 (Procell, PM150110) medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under 5% CO2.

extract_protocol:
Cellular total RNA was isolated according to the TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation.
The libraries were prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: For sodium fluoroacetate treatment, cells were grown to 80% confluence in the 10-cm plastic dishes, then incubated with 10 mM sodium fluoroacetate (self-synthesized) for 6 h. RNAs containing Fac4C (10 μg in 10 μl nuclease-free water) and 2 μl probes (40 mM in DMF, self-synthesized) were performed in 40 μl reaction buffer containing 4 μl Tris buffer (1 M in nuclease-free water, pH 8.5) with TCEP (50 mM). DBCO-S-S-biotin (Click Chemistry Tools, A112-10) or DBCO-Cy5 was added into the system for click reaction to a final concentration of 20 mM and incubated at 37 °C for 2 h.  For Nat10 inhibition, when HeLa cells were grown to 80% confluence, 50 μM Nat10 inhibitor (Remodelin, MedChemExpress, HY-16706) was added into the cells and maintained for 16  h at 37 ℃ followed by fluoroacetate treatment. For Adriamycin treatment, cells were grown to 80% confluence in the 10-cm plastic dishes, then incubated with 0.25 μM Adriamycin (Aladdin, A183027) for 24 h.

value: Hela

tag: enrichment method


title: day 0 - replicate 1 AS-367951-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367949-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367963-LR-45389

description: day 0 - replicate 1


title: Hela, no sodium fluoroacetate treatment, rep1


title: HBC MG Sample #1 (23HBC)


title: day 0 - replicate 1 AS-367947-LR-45389

description: day 0 - replicate 1


title: Brain, Alzheimer’s Disease, sample 15

city: Philadelphia

first: Edward

last: Lee

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

description:
10x Genomics
AdsnRNAseq_GEO.h5ad
Microglia_GEO.h5ad
Astrocytes_GEO.h5ad

data_processing:
Reads, including intronic reads, were aligned to the hg38 genome sequence (GRCh38.p12) using CellRanger (v.3.0.2)
Nuclei were filtered to remove likely doublets and poor quality data. Nuclei were kept if (i) the number of expressed genes is between 200 and 4000 and (ii) mitochondrial gene UMI proportion is less than 5%. Genes expressed in less than ten cells were removed from further analysis.
Nuclei were clustered based on 2000 highly variable genes using DESC, an unsupervised deep-embedding algorithm for iterative single-cell clustering. Nuclei were clustered to 15 different resolutions and annotated based on known marker genes for microglia, endothelial cells, excitatory neurons, inhibitory neurons, astrocytes, oligodendrocytes, and oligodendrocyte progenitor cells. Nuclei with consistent cell type annotations across clustering resolutions were kept for downstream analysis.
Microglia and astrocytes were subset and further clustered to identify microglia and astrocyte subpopulations
Assembly: hg38
Supplementary files format and content: AdsnRNAseq_GEO.h5ad: AnnData containing nuclei read count matrix, nuclei annotations, and sample metadata for full dataset
Supplementary files format and content: Microglia_GEO.h5ad: AnnData containing nuclei read count matrix, nuclei annotations, and sample metadata for microglia
Supplementary files format and content: Astrocytes_GEO.h5ad: AnnData containing nuclei read count and CarDEC-denoised gene expression matrices, nuclei annotations, and sample metadata for astrocytes

molecule: nuclear RNA

source_name: dorsolateral prefrontal cortex

extract_protocol:
Frozen middle frontal neocortex brain tissue was transferred to a pre-chilled dounce homogenizer. Homogenization buffer consisted of 0.25 M sucrose in TKM buffer (50 mM Tris–HCl, pH 7.5, 25 mM KCl, 14 mM MgCl2, and 0.4 U/uL RNAse inhibitor and was added to the dounce homogenizer, at a ratio of 2 mL buffer per 125 mg of tissue. The homogenate was mixed with 2.3 M sucrose + TKM solution to generate a 1.6 M sucrose solution in a chilled ultracentrifuge tube pre-filled with 3 mL cushion buffer (1.8 M sucrose in TKM) and spun at 100,000×g for 45 min at 4 °C in a swinging bucket rotor (Sw-41Ti rotor on an XPN-80 ultracentrifuge). After ultracentrifugation, the myelin layer was removed, the supernatant aspirated and discarded, and the remaining pellet was re-suspended in 1X PBS and RNAsin Plus RNAse inhibitor.
Library construction was performed by the Center for Applied Genomics Sequencing Core at the Children’s Hospital of Philadelphia in accordance with manufacturer’s (10x Genomics) instructions.

value: dorsolateral prefrontal cortex

tag: apoe genotype

tag: trem2 genotype

tag: amyloid tau_(at)_pathology_score

value: A+T+


title: day 0 - replicate 1 AS-367957-LR-45389

description: day 0 - replicate 1

tag: tissue