title: Organoid 5D4

description:
Kidney
5D4_S28


title: Organoid 5H3

status: Public on Dec 15 2023

type: SRA

city: London

first: Mattia

middle: Francesco Maria

last: Gerli

address: Rowland hill street

department: Department of Surgical Biotechnology

country: United Kingdom

institute: University College London

description:
Kidney
5H3_S24

library_source: transcriptomic

data_processing:
scRNAseq: v6.0.1 CellRanger for processing, with v4.2.0 Seurat was used for analysis. Bulk: Quality control was conducted on the FASTQ raw sequences using v0.11.9 FastQC (https://github.com/s-andrews/FastQC). v0.6.6 TrimGalore! (https://github.com/FelixKrueger/TrimGalore) was used to trim low quality reads (quality 20, length 70). v2.7.1a STAR (https://github.com/alexdobin/STAR) was applied to align the FASTQ sequences to the NCBI human reference genome GRCh38.p13 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39/). v1.6.3 featureCounts (https://doi.org/10.1093/bioinformatics/btt656) quantified the expression of individual genes to generate the raw count matrix, using the GRCh38.104 gene annotation (ensembl.org/Homo_sapiens/Info/Index). Default parameters used for both alignment and quantification. The generated count martrix was further processed with a custom R script. Genes will less than 10 reads across 3 samples were removed. Gene IDs were included using the added BioMart package (ensembl.org/info/data/biomart/biomart_r_package.html). Counts per million (CPM) normalisation was completed with the edgeR package (bioconductor.org/packages/release/bioc/html/edgeR.html). ComBat_seq batch correction (rdrr.io/bioc/sva/man/ComBat_seq.html) was applied between the 4 batches.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: scRNAseq: None. Bulk: Viable amniotic fluid cells were resuspended in 30 μL of Matrigel (Corning) and plated 6x105 live cells/droplet onto a pre-warmed 24 well plate. Cells were cultured in an ad hoc defined generic medium (Supplementary Table 2) supplemented with Rho-kinase inhibitor (ROCKi; Tocris) and Primocin. To establish clonal organoid lines, single organoids formed were manually picked at passage 0 under the microscope to be clonally expanded. Each organoid was transferred in a 0.5 mL tube pre-coated with 1% BSA. After centrifugation the pellet was resuspended in 20 μL Matrigel (Corning). The plate was incubated for 20 min at 37°C and generic medium was added with ROCKi (Tocris) and Primocin for the first 3 days. Medium was replaced every 3-4 days. After approximately 10 days, grown organoids were passaged.

extract_protocol:
Bulk: RNA was harvested using Rneasy mini plus kit (Qiagen). scRNAseq: No extraction
Bulk: NEBNext Low Input RNA library preparation. scRNAseq: 10x Chromium 3' v3.1
Bulk: Single-end RNA-seq. scRNAseq: Single-end RNA-seq

tag: cell line

tag: cell type

value: Amniotic Fluid-derived Organoids

tag: treatment

value: Before-FETO

tag: time


title: Organoid 5B1

description:
Lung
5B1_S2


title: Organoid 5B4

description:
Lung
5B4_S26


title: Organoid 5A4

description:
Lung
5A4_S25


title: Organoid 5E5

description:
Lung
5E5_S37

value: Tracheal Fluid-derived Organoids

value: After-FETO


title: Organoid 5A6

description:
Lung
5A6_S41


title: Organoid 5E6

description:
Lung
5E6_S45


title: Organoid 5A3

description:
Lung
5A3_S17


title: Organoid 5E4

description:
Lung
5E4_S29


title: Organoid H1

description:
Kidney
H1_S8


title: Organoid 40D9

description: Lung

data_processing:
scRNAseq: Seurat. Bulk: Quality control was conducted on the FASTQ raw sequences using v0.11.9 FastQC (https://github.com/s-andrews/FastQC). v0.6.6 TrimGalore! (https://github.com/FelixKrueger/TrimGalore) was used to trim low quality reads (quality 20, length 70). v2.7.1a STAR (https://github.com/alexdobin/STAR) was applied to align the FASTQ sequences to the NCBI human reference genome GRCh38.p13 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39/). v1.6.3 featureCounts (https://doi.org/10.1093/bioinformatics/btt656) quantified the expression of individual genes to generate the raw count matrix, using the GRCh38.104 gene annotation (ensembl.org/Homo_sapiens/Info/Index). Default parameters used for both alignment and quantification. The generated count martrix was further processed with a custom R script. Genes will less than 10 reads across 3 samples were removed. Gene IDs were included using the added BioMart package (ensembl.org/info/data/biomart/biomart_r_package.html). Counts per million (CPM) normalisation was completed with the edgeR package (bioconductor.org/packages/release/bioc/html/edgeR.html). ComBat_seq batch correction (rdrr.io/bioc/sva/man/ComBat_seq.html) was applied between the 4 batches.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample


title: Organoid 5A7

description:
Small Intestine
5A7_S49


title: Organoid 4Eone

description: Lung


title: Organoid SI23w

description: Small Intestine

value: Fetal Tissue-derived Control Organoids


title: Organoid SI18w

description: Small Intestine


title: Organoid 67D11

description: Small Intestine


title: Organoid 46D12

description: Small Intestine


title: Organoid 4D3

description: Lung


title: Organoid 5B7

description:
Lung
5B7_S50


title: Organoid 4C8

description: Lung


title: Organoid 4C6

description: Lung


title: Organoid K22wA

description: Kidney


title: Organoid 4C9

description: Lung

tag: genotype

value: CDH


title: Organoid 4D2

description: Kidney


title: Organoid 4C5

description: Small Intestine


title: Organoid 4C7

description: Lung


title: Organoid 4C11

description: Kidney


title: Organoid K22wB

description: Kidney


title: Organoid 4B6

description: Lung


title: Organoid 4C4

description: Kidney


title: Organoid 4B9

description: Lung


title: Organoid 4C1

description: Small Intestine


title: Organoid 4B5

description: Kidney


title: Organoid 4B7

description: Lung


title: Organoid 4C2

description: Lung


title: Organoid 4C10

description: Lung


title: Organoid 4B2

description: Lung


title: Organoid 4B11

description: Lung


title: Organoid 4B1

description: Kidney


title: Organoid 4B3

description: Lung


title: Organoid 5G4

description:
Kidney
5G4_S31


title: Organoid 4B10

description: Lung


title: Organoid 4C3

description: Lung


title: Organoid 4A7

description: Kidney


title: Organoid 4A9

description: Kidney


title: Organoid 4B12

description: Small Intestine


title: Organoid 4B4

description: Lung


title: Organoid 4A8

description: Kidney


title: Organoid 4A3

description: Kidney


title: Organoid 4A4

description: Lung


title: Organoid 4A2

description: Kidney


title: Organoid 4A12

description: Lung


title: Organoid 4A5

description: Kidney


title: Organoid 4A11

description: Lung


title: Organoid 4A1

description: Kidney


title: Organoid 4A10

description: Kidney


title: Organoid 34D10

description: Small Intestine


title: Organoid SI10w

description: Small Intestine


title: Organoid H5

description: Lung


title: Organoid 28D7

description: Lung


title: Organoid 30D8

description: Lung


title: Organoid L20w

description: Lung


title: Organoid L18w

description: Lung


title: Organoid H4

description: Lung


title: Organoid G4

description: Lung


title: Organoid G7

description: Small Intestine


title: Organoid G3

description: Lung


title: Organoid G2

description: Lung


title: Organoid F6

description: Kidney


title: Organoid H3

description: Lung


title: Organoid F7

description: Small Intestine


title: Organoid F5

description: Lung


title: Organoid F3

description: Lung


title: Organoid F4

description: Lung


title: Organoid G1

description: Kidney


title: Organoid F1

description: Lung


title: Organoid F2

description: Kidney


title: Organoid E6

description: Kidney


title: Organoid E5

description: Lung


title: Organoid E2

description: Kidney


title: Organoid E3

description: Lung


title: Organoid E4

description: Lung


title: Organoid E1

description: Lung


title: Organoid 4B8

description: Lung


title: Organoid D7

description: Small Intestine


title: Organoid D5

description: Lung


title: Organoid D4

description: Lung


title: Organoid D6

description: Lung


title: Organoid D3

description: Lung


title: Organoid H2

description: Lung


title: Organoid D2

description: Lung


title: Organoid 5E3

description:
Lung
5E3_S21


title: Organoid C5

description: Lung


title: Organoid C4

description: Lung


title: Organoid C3

description: Lung


title: Organoid C2

description: Lung


title: Organoid B5

description: Lung


title: Organoid B2

description: Lung


title: Organoid B3

description: Lung


title: Organoid B4

description: Lung


title: Organoid E7

description: Small Intestine


title: Organoid B1

description: Kidney


title: Organoid A7

description: Lung


title: Organoid A5

description: Lung


title: Organoid A4

description: Lung


title: Organoid A3

description: Lung


title: Organoid A2

description: Kidney


title: Organoid A1

description: Kidney


title: Organoid S13w

description: Stomach


title: Organoid L11w

description: Lung


title: Organoid L16w

description: Lung


title: Organoid D1

description: Kidney


title: Organoid S22w

description: Stomach


title: Organoid 8

description: Lung


title: Organoid B7

description: Kidney


title: Organoid 74

description: Lung


title: Organoid 72

description: Lung


title: Organoid 71

description: Lung


title: Organoid 9

description: Lung


title: Organoid C1

description: Kidney


title: Organoid K16w

description: Kidney


title: Organoid 69

description: Small Intestine


title: Organoid 68

description: Small Intestine


title: Organoid 65

description: Lung


title: Organoid 64

description: Kidney


title: Organoid 63

description: Kidney


title: Organoid 61

description: Kidney


title: Organoid 66

description: Small Intestine


title: Organoid 7

description: Lung


title: Organoid 60

description: Kidney


title: Organoid 62

description: Kidney


title: Organoid 6

description: Lung


title: Organoid S20w

description: Stomach


title: Organoid SI13w

description: Small Intestine


title: Organoid 59

description: Kidney


title: Organoid 58

description: Small Intestine


title: Organoid 55

description: Small Intestine


title: Organoid 57

description: Small Intestine


title: Organoid 73

description: Lung


title: Organoid 54

description: Small Intestine


title: Organoid 52

description: Lung


title: Organoid 70

description: Kidney


title: Organoid 53

description: Small Intestine


title: Organoid 5

description: Kidney


title: Organoid 4A6

description: Kidney


title: Organoid 48

description: Kidney


title: Organoid 51

description: Lung


title: Organoid 50

description: Lung


title: Organoid 47

description: Kidney


title: Organoid 49

description: Kidney


title: Organoid 44

description: Small Intestine


title: Organoid 45

description: Small Intestine


title: Organoid 43

description: Small Intestine


title: Organoid 41

description: Lung


title: Organoid 4

description: Kidney


title: Organoid 39

description: Kidney


title: Organoid 37

description: Kidney


title: Organoid 38

description: Lung


title: Organoid 36

description: Small Intestine


title: Organoid 35

description: Small Intestine


title: Organoid 56

description: Small Intestine


title: Organoid 3

description: Lung


title: Organoid 32

description: Lung


title: Organoid 25

description: Kidney


title: Organoid 26

description: Kidney


title: Organoid 29

description: Lung


title: Organoid 23

description: Small Intestine


title: Organoid 24

description: Kidney


title: Organoid 27

description: Kidney


title: Organoid 31

description: Kidney


title: Organoid 21

description: Small Intestine


title: Organoid 20

description: Lung


title: Organoid 2

description: Kidney


title: Organoid 18

description: Lung


title: Organoid 15

description: Kidney


title: Organoid 16

description: Lung


title: Organoid 19

description: Lung


title: Organoid 14

description: Lung


title: Organoid 13

description: Kidney


title: Organoid 1

description: Kidney


title: Organoid 11

description: Small Intestine


title: Organoid 10

description: Small Intestine


title: Organoid R

description: Kidney

source_name: R

value: R


title: Organoid M

description: Lung

source_name: M

value: M


title: Organoid L

description: Lung

source_name: L

value: L


title: Organoid P

description: Lung

source_name: P

value: P


title: Organoid J

description: Lung

source_name: J

value: J


title: Organoid 22

description: Small Intestine


title: Organoid K

description: Lung

source_name: K

value: K


title: Organoid I

description: Lung

source_name: I

value: I


title: Organoid Q

description: Lung

source_name: Q

value: Q


title: Organoid C

description: Lung

source_name: C

value: C


title: Organoid H

description: Lung

source_name: H

value: H


title: Organoid B

description: Lung

source_name: B

value: B


title: Organoid F

description: Lung

source_name: F

value: F

value: Amniotic Fluid-derived Organoids


title: Organoid E

description: Lung

source_name: E

value: E


title: Organoid 17

description: Lung


title: Organoid O

description: Lung

source_name: O

value: O


title: Organoid 12

description: Kidney


title: Organoid D

description: Lung

source_name: D

value: D


title: Perturb_Ch5_Foxgdialout

status: Public on Dec 05 2023

city: San Diego

first: Xinhe

last: Zheng

state: California

address: 3528 General Atomics Court

department: Neuroscience

country: USA

institute: The Scripps Research Institute

description:
Perturb_all.qs
Perturb_sg.qs

library_source: transcriptomic single cell

data_processing:
BCL files of transcriptome libraries were used to generate FASTQ files using the default parameters by “cellranger mkfastq” command (Cell Ranger v7.1.0). The gRNA library or AAV barcode dial-out library was demultiplexed using bcl2fastq.
The “cellranger count” command was used to align the transcriptome reads to the mouse genome reference mm10 (GENCODE vM23/Ensembl 98) and generate a gene expression count matrix, using expect-cells = 9,000. The AAV barcodes or gRNA reads were quantified at the single-cell level with the feature-ref flag in Cell Ranger.
Assembly: mm10
Supplementary files format and content: Robj or QS file of gene-cell matrix

organism: Mus musculus

source_name: Cortex

growth_protocol: All animal experiments were performed according to protocols approved by the Institutional Animal Care and Use Committees (IACUC) of The Scripps Research Institute

extract_protocol:
Tissue dissociation was performed with the Papain Dissociation kit (Worthington, #LK003150) in a modification of a previously described protocol. Briefly, young mice were anesthetized then disinfected with 70% ethanol and decapitated. The brains were quickly extracted and gently dabbed with a PBS-soaked Kimwipe (Kimberly-Clark) to remove the meninge and fibroblasts. Cortices were micro-dissected in ice-cold dissection medium (Hibernate A medium (Thermo Fisher Scientific, #A1247501) with B27 supplement (Thermo Fisher Scientific, #17504044) and Trehalose (Sigma Aldrich, Cat# T9531) under a dissecting microscope. Microdissected cortices were transferred into papain solution with DNase in a cell culture dish and cut into small pieces with a razor blade. The dish was then placed onto a digital rocker in a cell culture incubator for 30 mins with rocking speed at 30 rpm at 37°C. The digested tissues were collected into a 15 mL tube and triturated with a 10 mL low bind plastic pipette 20 times and the cell suspension was carefully transferred to a new 15 mL tube. 2.7 mL of EBSS, 3 mL of reconstituted Worthington inhibitor solution, and DNase solution were added to the 15 mL tube and mixed gently. Cells were pelleted by centrifugation at 300 g for 5 mins at 4°C, followed by washing with 8ml cold dissection medium at 200g for 5 min at 4°C. Cells were resuspended in 0.5 mL ice-cold dissection medium with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, #16000069) and SYTOX dead cell stain (Invitrogen, #S34859), and subjected to FACS purification using Sony cell sorter (SH800).
scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3' Solution v3.1 kit with Feature Barcode Technology or the Chromium Next GEM Single Cell 5’ Solution v2 kit with Feature Barcode Technology (10x Genomics) following the manufacturer’s protocol.

treatment_protocol: AAV was administered in utero to the lateral ventricle at E13.5-14.5 in Cas9 transgenic mice (Jax#026179)

tag: tissue

value: Cortex

tag: age

value: AAV-SCH9-hypPB and gRNA library injected into lateral ventricle at E14.5


title: Perturb_Ch3_Foxgdialout

description:
Perturb_all.qs
Perturb_sg.qs


title: SRC107

status: Public on Dec 12 2023

city: Stanford

first: Ajay

last: Subramanian

state: CA

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

description: Spatial Gene Expression

data_processing:
Sample demultiplexing, tissue and fiducial detection, read alignment, and generation of feature-barcode matrices was performed using Space Ranger v1.3.0 (10x Genomics).
Assembly: GRCh38.
Supplementary files format and content: Raw feature barcode matrix for downstream analysis.

source_name: Leiomyosarcoma

extract_protocol:
Fresh sarcoma specimens were harvested and frozen in optimal cutting temperature compound (OCT). Sarcoma specimens were cryosectioned at -20 C onto gene expression slides and permeabilization time was optimized using 10 um sections with the Visium Spatial Tissue Optimization Slide & Reagents kit (10x Genomics).
Sequencing libraires were produced using the Visium Spatial Gene Expression Slide & Reagent kit (10x Genomics) according to the manufacturer’s instructions.
Spatial transcriptomics.

value: Leiomyosarcoma

value: Tumor


title: Perturb_Ch2_Foxgdialout

description:
Perturb_all.qs
Perturb_sg.qs


title: SRC106

description: Spatial Gene Expression

source_name: Undifferentiated pleomorphic sarcoma

value: Undifferentiated pleomorphic sarcoma


title: SRC95

description: Spatial Gene Expression


title: Perturb_Ch4_Foxgdialout

description:
Perturb_all.qs
Perturb_sg.qs


title: Perturb_Ch5

description:
Perturb_all.qs
Perturb_sg.qs


title: Perturb_Ch1_Foxgdialout

description:
Perturb_all.qs
Perturb_sg.qs


title: SRC93

description: Spatial Gene Expression


title: Organoid G

description: Lung

source_name: G

value: G


title: Perturb_Ch2

description:
Perturb_all.qs
Perturb_sg.qs


title: SCH9_P9_5p

description:
3p5p_all.Robj
3p5p_ctxobj.Robj

molecule: polyA RNA

value: AAV-SCH9-hypPB and tdTomato-KASH injected into lateral ventricle at E14.5


title: SCH9_P9_3p

description:
3p5p_all.Robj
3p5p_ctxobj.Robj


title: Organoid A

description: Lung

source_name: A

value: A


title: AAVlib2_E15_unsort

description:
AAV_all.Robj
AAV_ctxobj.Robj

source_name: Forebrain

value: Forebrain

value: 14 serotype AAV library injected into lateral ventricle at E13.5, all cortical cells


title: AAVlib2_E15_sort

description:
AAV_all.Robj
AAV_ctxobj.Robj

value: 14 serotype AAV library injected into lateral ventricle at E13.5, transduced cells


title: fHDF/TERT166 rep 1 [P8601_113]

status: Public on Aug 21 2023

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
Raw sequences were mapped to the human reference genome GRCh38 and further quantified using the Kallisto (v0.46.2).
Transcript abundances were aggregated into gene level as transcripts per million (TPM) by tximport (v1.22.0)
Only protein-coding genes and transcripts were included for downstream analysis, resulting in 20,090 genes analyzed.
Assembly: GRCh38.p13 (Ensembl build 103.38)
Supplementary files format and content: A tab separated text file containing gene expression TPM for each sample.

source_name: Foreskin

growth_protocol: All cell lines were cultivated at 37°C in a 5% CO2humidified environment in growth media. Details can be found at https://doi.org/10.1126/science.aal3321.

extract_protocol:
RNA was extracted from the cells using the RNeasy kit (Qiagen).
Samples with high-quality total RNA (i.e., RIN > 8)  were used as input material for library construction with Illumina TruSeq Stranded mRNA reagents.

value: Foreskin

value: WT


title: fHDF/TERT166 rep 2 [P8601_114]


title: HHSteC rep 1 [P8601_115]

source_name: Liver

value: Liver

value: HHSteC


title: HSkMC rep 2 [P8601_112]

source_name: Muscle

value: Muscle

value: HSkMC


title: HAP1 rep 1 [P8601_109]

source_name: Bone marrow

value: Bone marrow


title: HHSteC rep 2 [P8601_116]


title: HSkMC rep 1 [P8601_111]


title: hTEC/SVTERT24-B rep 2 [P8601_104]

source_name: Thymus

value: Thymus


title: hTEC/SVTERT24-B rep 1 [P8601_103]


title: hTERT-HME1 rep 2 [P8601_102]

source_name: Breast

value: Breast


title: hTERT-HME1 rep 1 [P8601_101]


title: ASC diff rep 1 [P8601_105]

source_name: Adipose

value: Adipose

value: ASC diff


title: AF22 rep 1 [P809_101]

source_name: Skin

value: Skin


title: Perturb_Ch4

description:
Perturb_all.qs
Perturb_sg.qs

value: Cortex

value: AAV-SCH9-hypPB and gRNA library injected into lateral ventricle at E14.5


title: Perturb_Ch1

description:
Perturb_all.qs
Perturb_sg.qs


title: HBEC3-KT rep 2 [P8601_108]

source_name: Bronchus

value: Bronchus


title: HBEC3-KT rep 1 [P8601_107]


title: HBF/TERT88 rep 2 [P4802_112]

source_name: Brain

value: Brain


title: Perturb_Ch3

description:
Perturb_all.qs
Perturb_sg.qs


title: HBF/TERT88 rep 1 [P4802_111]


title: LHCN-M2 rep 2 [P4802_110]


title: LHCN-M2 rep 1 [P4802_109]


title: hTCEpi rep 2 [P4802_108]

source_name: Eye

value: Eye

value: hTCEpi


title: Physcomitrella patens plate culture 5GRO-seq r1

status: Public on Sep 28 2023

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
5'GRO-seq; nascent TSS mapping in P.patens cells; Experiment SD150
P.patens-Gransden-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: 5'GRO-seq

organism: Physcomitrium patens

source_name: plate culture

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol:
nuclei for the 5'GRO-seq were extracted as described in (J. Hetzel et al. 2016)
5'GRO-seq was performed as described in (J. Hetzel et al. 2016)

value: plate culture


title: hTCEpi rep 1 [P4802_107]

value: WT


title: RPTEC/TERT1 rep 2 [P4802_106]

source_name: Kidney

value: Kidney


title: HAP1 rep 2 [P8601_110]


title: HUVEC/TERT2 rep 2 [P4802_105]

source_name: Umbilical vein

value: Umbilical vein


title: ASC52telo rep 2 [P4802_102]


title: RPTEC/TERT1 rep 1 [P4802_103]


title: HUVEC/TERT2 rep 1 [P4802_104]


title: ASC52telo rep 1 [P4802_101]


title: BJ1-hTERT rep 2 [P3808_113]

value: Foreskin


title: BJ hTERT+ SV40 Large T+ RasG12V rep 2 [P3808_114]

value: BJ hTERT+ SV40 Large T+ RasG12V


title: AF22 rep 2 [P809_102]


title: BJ hTERT+ SV40 Large T+ rep 2 [P3808_111]

value: BJ hTERT+ SV40 Large T+


title: BJ hTERT+ SV40 Large T+ rep 1 [P3808_105]


title: RPMI-8226 rep 2 [P262_209]

source_name: Peripheral blood

value: Peripheral blood


title: NB4 rep 2 [P262_210]

value: Bone marrow


title: BeWo rep 2 [P262_208]

value: BeWo


title: BJ1-hTERT rep 1 [P3808_103]


title: NB4 rep 1 [P262_205]


title: SH-SY5Y rep 2 [P262_211]


title: SH-SY5Y rep 1 [P262_207]


title: BeWo rep 1 [P262_204]


title: U-2197 rep 2 [P262_203]

source_name: Subcutis

value: Subcutis


title: SCLC-21H rep 2 [P262_206]

source_name: Pleural effusion

value: Pleural effusion


title: Reh rep 1 [P262_196]

value: Reh


title: Reh rep 2 [P262_201]


title: MOLT-4 rep 2 [P262_194]


title: U-2197 rep 1 [P262_202]


title: SCLC-21H rep 1 [P262_195]


title: U2OS rep 3 [P262_190]

source_name: Bone

value: Bone


title: U2OS rep 4 [P262_191]


title: RPMI-8226 rep 1 [P262_189]


title: SK-BR-3 rep 2 [P262_188]


title: HMC-1 rep 2 [P262_186]


title: SK-BR-3 rep 1 [P262_187]


title: MOLT-4 rep 1 [P262_193]


title: NTERA-2 rep 1 [P262_184]

source_name: Lung

value: Lung


title: WM115 rep 2 [P262_183]

value: Skin


title: NTERA-2 rep 2 [P262_185]


title: U-138MG rep 2 [P262_182]

value: Brain


title: BJ hTERT+ SV40 Large T+ RasG12V rep 1 [P3808_107]

source_name: Foreskin


title: T-47D rep 1 [P262_174]


title: AN3-CA rep 2 [P262_180]

source_name: Lymph node

value: Lymph node


title: AN3-CA rep 1 [P262_179]

value: WT


title: U-266/70 rep 2 [P262_178]


title: Capan-2 rep 2 [P262_176]

source_name: Pancreas

value: Pancreas


title: Capan-2 rep 1 [P262_175]


title: U-266/70 rep 1 [P262_177]


title: WM115 rep 1 [P262_172]


title: HaCaT rep 2 [P262_169]

value: HaCaT


title: HMC-1 rep 1 [P262_173]


title: U-87MG ATCC rep 2 [P262_167]

value: U-87MG ATCC


title: HaCaT rep 1 [P262_168]


title: BJ [Human fibroblast] rep 2 [P253_102]

value: Foreskin

value: BJ [Human fibroblast]


title: U-87MG ATCC rep 1 [P262_166]


title: BJ [Human fibroblast] rep 1 [P253_101]


title: U-698-M rep 4 [P189_140]

source_name: Tonsil

value: Tonsil


title: U-698-M rep 3 [P189_139]


title: A-431 rep 1 [P189_141]


title: U2OS rep 2 [P189_146]


title: A-431 rep 2 [P189_142]


title: U2OS rep 1 [P189_145]


title: U-138MG rep 1 [P262_181]


title: SK-MEL-30 rep 2 [P189_138]


title: SK-MEL-30 rep 1 [P189_137]


title: U-937 rep 3 [P189_133]


title: THP-1 rep 1 [P189_135]

value: Peripheral blood


title: U-266/84 rep 2 [P189_132]


title: Karpas-707 rep 1 [P262_170]

source_name: Bone marrow

value: Bone marrow


title: U-266/84 rep 1 [P189_131]


title: THP-1 rep 2 [P189_136]


title: HDLM-2 [P189_130]


title: Karpas-707 rep 2 [P262_171]


title: EFO-21 rep 2 [P189_129]

source_name: Ascites

value: Ascites


title: EFO-21 rep 1 [P189_128]


title: SuSa rep 1 [P12220_109]

source_name: Testis

value: Testis

value: SuSa


title: SuSa rep 2 [P12220_110]


title: hTERT-RPE1 rep 2 [P12220_108]

value: Eye


title: U-251MG rep 1 [P189_143]

source_name: Brain


title: hTERT-RPE1 rep 1 [P12220_107]

source_name: Eye


title: OE19 rep 2 [P12220_106]

source_name: Esophagus

value: Esophagus


title: OE19 rep 1 [P12220_105]


title: Jurkat rep 2 [P12220_102]

value: Jurkat


title: Jurkat rep 1 [P12220_101]


title: U-937 rep 2 [P000_040]

value: Pleural effusion


title: GaMG rep 1 [P12220_103]

value: Brain

value: GaMG


title: GaMG rep 2 [P12220_104]

value: WT


title: U-698-M rep 2 [P000_038]


title: ASC diff rep 2 [P8601_106]

source_name: Adipose

value: Adipose

value: ASC diff


title: U-937 rep 1 [P000_039]


title: U-698-M rep 1 [P000_037]


title: Rh30 rep 1 [P000_034]


title: HL-60 rep 2 [P000_033]


title: Rh30 rep 2 [P000_035]


title: U-937 rep 4 [P189_134]


title: SiHa [P000_036]

source_name: Cervix

value: Cervix

value: SiHa


title: K-562 rep 2 [P000_022]


title: TIME [P000_027]

value: Foreskin

value: TIME


title: HEL rep 2 [P000_020]

source_name: Peripheral blood

value: Peripheral blood

value: HEL


title: HEL rep 1 [P000_019]


title: HL-60 rep 1 [P000_032]


title: Daudi rep 2 [P000_018]

value: Daudi


title: RT-4 rep 2 [P000_016]

source_name: Urinary bladder

value: Urinary bladder


title: RT-4 rep 1 [P000_015]


title: Daudi rep 1 [P000_017]


title: HEK293 rep 1 [P000_011]

source_name: Fetal kidney

value: Fetal kidney


title: HeLa rep 2 [P000_014]

value: HeLa


title: HeLa rep 1 [P000_013]


title: HEK293 rep 2 [P000_012]


title: Hep-G2 rep 1 [P000_007]

source_name: Liver

value: Liver


title: Hep-G2 rep 2 [P000_008]


title: Caco-2 rep 1 [P000_005]

source_name: Colon

value: Colon


title: PC-3 rep 2 [P000_010]

source_name: Bone

value: Bone


title: A-549 rep 2 [P000_004]

source_name: Lung

value: Lung


title: Caco-2 rep 2 [P000_006]

value: WT


title: K-562 rep 1 [P000_021]

source_name: Pleural effusion

value: Pleural effusion


title: A-549 rep 1 [P000_003]


title: MCF-7 rep 2 [P000_002]


title: MCF-7 rep 1 [P000_001]


title: V11M22-398-C1

status: Public on Aug 11 2023

city: Berkeley

first: Benjamin

last: Cole

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

description: 10x Genomics Visium

data_processing:
For spatial transcriptomics samples, demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v2.1.1 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: Medicago truncatula MedtrA17_4.0, Rhizophagus irregularis Rir_HGAP_ii_V2 (DAOM 181602, DAOM 197198)
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz:  list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: Tab-separated values files and matrix files

organism: Medicago truncatula

source_name: root

growth_protocol: Seeds of Medicago truncatula Gaertn, cv Jemalong A17 (Noble Foundation) were scarified in concentrated sulfuric acid for 5-10 min and rinsed with distilled water, sterilized in 3.75% sodium hypochlorite solution, then rinsed five times with sterile distilled water and placed on 1â„2 Murashige and Skoog medium, 1% agar plates at 4C or RT for 48h. Germinated seedlings were transplanted to the top fine sand layer of inoculated and non-inoculated sand cones. Plants were grown in 22-24 ËšC 16 h day/ 8 h night, with 300 Î¼mol m-2 s-1 light intensity, and 60% relative humidity.

extract_protocol:
150 mg of roots growing in inoculated fine sand layer was weighed out and placed in the lid of a petri dish and chopped rapidly with a razor blade for three minutes in 600ÂµL NIBAM: 1x NIB (Sigma CELLYTPN1-1KT), 4% BSA, 1 mM DTT, 0.4 U/ÂµL Superase RNAse inhibitor (Sigma), 1:100 Protease Inhibitor Cocktail for plant tissues (Sigma). NIBAM-root slurry was strained through 40 Âµm and 20 Âµm filters (CellTrics). SYBR Green (1:10000) was used to visualize nuclei during purification on the Influx Flow Cytometer.
Library was performed according to the manufacterâ€™s instructions (10X Genomics, Visium Spatial Gene Expression Slide & Reagent Kit). Briefly, the pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
Visium spatial transcriptomics

treatment_protocol: To inoculate seedlings with Rhizophagus irregularis (BÅ‚aszk., Wubet, Renker and Buscot) C. Walker and A. SchÃ¼ÃŸler: 50 mL Agtiv Field Crops liquid mycorrhizal inoculant (PremierTech, RiviÃ¨re-du-Loup, QuÃ©bec, Canada) spores were captured on a 40 Âµm filter, rinsed with distilled water and resuspended in 50 mL distilled water. 1 mL of resuspended spores was applied to the horticultural sand layer and an additional 300 ÂµL applied to the fine play sand layer.

value: root

value: not inoculated

tag: timepoint

tag: strain


title: V11M22-398-B1

description: 10x Genomics Visium

value: Medicago truncatula Gaertn, cv Jemalong A17


title: V11M22-398-D1

description: 10x Genomics Visium


title: V11M22-398-A1

description: 10x Genomics Visium


title: V11M22-399-C1

description: 10x Genomics Visium


title: V11M22-399-D1

description: 10x Genomics Visium


title: V11M22-399-A1

description: 10x Genomics Visium


title: V11M22-399-B1

description: 10x Genomics Visium


title: V11M22-401-D1

description: 10x Genomics Visium

value: inoculated with Rhizophagus irregularis DAOM 181602, DAOM 197198


title: V11M22-401-C1

description: 10x Genomics Visium


title: V11M22-401-B1

description: 10x Genomics Visium


title: V11Y10-339-D1

description: 10x Genomics Visium


title: V11Y10-339-A1

description: 10x Genomics Visium


title: V11Y10-339-B1

description: 10x Genomics Visium


title: V11M22-401-A1

description: 10x Genomics Visium


title: V11Y10-339-C1

description: 10x Genomics Visium


title: V11Y10-341-D1

description: 10x Genomics Visium


title: V11Y10-341-B1

description: 10x Genomics Visium


title: V11Y10-341-A1

description: 10x Genomics Visium


title: HPAC cells scramble expressing vector replicate 2

status: Public on Aug 08 2023

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: HPAC

growth_protocol: HPAC cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HPAC

value: Pancreatic cancer cells

value: Wild type


title: V11Y10-341-C1

description: 10x Genomics Visium


title: HPAC cells scramble expressing vector replicate 1


title: HPAC cells scramble expressing vector replicate 3


title: TO_1N_2

status: Public on Jul 26 2023

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Raw data files were aligned to the reference genome and the mirbase database using Torrent Suite default parameters.
Assembly: hg19

source_name: Plasma

extract_protocol:
Plasma was isolated from EDTA or Lithium Heparin blood samples within 1 hour from collection, with a standard procedure to prevent haemolysis.
Total RNA was extracted with miRNeasy serum/plasma kit (Qiagen) using Exiqon protocol, with the batteriophage MS2RNA carrier (Roche Diagnostics) to promote RNA precipitation and purification on membranes.
For library preparation, smallRNA enriched samples were converted in barcoded cDNA libraries following the Ion Total RNA-Seq kit v2 protocol (Thermo Fisher) with the recommendations for low input RNA quantity. First, RNA samples were enriched for smallRNA fraction using a magnetic bead-based technology. After hybridization and ligation steps, through which 3' and 5' adaptors are directionally and simultaneously attached, reverse transcription was performed to obtain cDNA. cDNA was subsequently purified and size selected and then amplified using barcoded primers (obtained from Ion Xpress™ RNA-Seq Barcode 01-16 Kit, Thermo Fisher or synthesized by Eurofins Genomics as custom oligonucleotides (barcodes 17-24)). Finally, libraries were purified with beads. All the purification steps were performed by means of the Magnetic Bead Cleanup Module included in the kit. Libraries were checked for yield and size distribution by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) and 24 differentially barcoded smallRNA libraries were pooled. Pools were checked by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) to determine the library dilution required for template preparation. Ion Chef™ System (Thermo Fisher) was used for automated templated Ion Sphere Particles preparation and chip loading. Ion 540 chips (Thermo Fisher) were sequenced using Ion GeneStudio S5 System (Thermo Fisher).

value: Plasma

tag: disease state

value: control


title: SCAT3_R1

status: Public on Jul 14 2023

city: Rochester

first: Laura

last: Calvi

state: New York

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing:
MultiQC v1.5
Data Formating
bcltofastq-2.19.0
Data Cleaning
Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment : using trimmed sequences
STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read quantification by subread-1.6.1, featurecounts
Assembly: Reference Genome
Assembly: GRCm38 + gencode M17
Supplementary files format and content: Tab delineated txt files

source_name: Bone marrow stromal cells

growth_protocol: Sorted mesenchymal-osteolineage cells were cultured in alpha-MEM without ascorbic, with Penn/strep and 10% FBS.

extract_protocol:
Cells were lysed using RLT plus buffer with BME. RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA

value: Bone marrow stromal cells

value: Mesenchymal Stromal Cell

value: wt

value: Apoptotic thymocyte fed 24hrs

value: 24 hours


title: SCAT2_R1


title: SC2_R1

value: Control


title: SC3_R1


title: 3hr_ST2_PMNpositive_3

description:
X3hr_ST2_PMNpositive_3
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice

data_processing:
MultiQC v1.7
Sequence reads were processed using FastP, An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
ST2: trimmed sequences were aligned using STAR_2.7.0f to reference genome - GRCm38.p6 + Gencode-M22 Annotation;
PMNonly: trimmed sequences were aligned using STAR 2.7.0f to reference genome GRCh38.p13 + Genocode-31 Annotation
Read quantification by subread-1.6.4, featurecounts
Assembly: ST2: M22

source_name: cell line

growth_protocol: ST2: ST2 mesenchymal stem cell line were maintained in alpha MEM minus ascorbic acid supplemented with 10% fetal bovin serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C,

extract_protocol:
Cells were lysed using RLT plus buffer with BME. RNA was harvested using Rneasy mini plus kit (Qiagen). 50ng of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA

treatment_protocol: ST2 cells were fed aged PMNs stained with eF670 membrane stain at a ratio of 10:1 (PMNs:ST2s) for 3hrs or 24hrs. ST2 cells were sorted as PMN positive based on eF670 uptake consistent with greater than or equal to whole target cell uptake (PMNs).

value: cell line

value: Bone marrow stromal cell

value: WT

value: PMN Fed 3hrs

value: 3 hours


title: 3hr_ST2_PMNpositive_1

description:
X3hr_ST2_PMNpositive_1
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: T-47D rep 2 [P262_192]

value: Pleural effusion


title: 24hr_ST2only_3

description:
X24hr_ST2only_3
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: 24hr_ST2only_2

description:
X24hr_ST2only_2
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: 24hr_ST2only_1

description:
X24hr_ST2only_1
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: SC1_R1


title: PC-3 rep 1 [P000_009]

value: Bone


title: 24hr_ST2_PMNpositive_3

description:
X24hr_ST2_PMNpositive_3
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice

value: PMN Fed 24hrs


title: 24hr_ST2_PMNpositive_1

description:
X24hr_ST2_PMNpositive_1
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: hbca_c39,P31,replicate_1,left,overnight_digestion

status: Public on Jun 29 2023

city: Houston

first: Nicholas

last: Navin

state: TX

address: 6767 Bertner Ave

department: System Biology

institute: MD Anderson Cancer Center

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c39
surgical sample

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: H5

source_name: breast

extract_protocol:
RNAs are extracted from single cells suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

value: breast

tag: paper participant_number

tag: assay

value: 10x Genomics 3' V3


title: 24hr_ST2_PMNpositive_2

description:
X24hr_ST2_PMNpositive_2
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice


title: hbca_c26,P20,replicate_1,NA,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c26
surgical sample


title: hbca_c38,P30,replicate_1,right,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c38
surgical sample


title: hbca_c31,P24,replicate_1,NA,6hr_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c31
surgical sample


title: hbca_c25,P20,replicate_1,NA,short_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c25
surgical sample


title: hbca_c32,P24,replicate_1,NA,overnight_digestion

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_c32
surgical sample


title: PDX LX831b osimertinib+lurbinectedin_ rep.4

status: Public on Jun 08 2023

city: New York

first: Triparna

last: Sen

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The human genome and transcriptome reference used is GRCh38.p13 genome assembly from GENCODE release 36. The alignment is performed by using STAR aligner (v2.7.5b). Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries using mapping mode.
Assembly: GRCh38.p13
Supplementary files format and content: Gene level read counts

source_name: Tumor tissue derived from lung

extract_protocol: A total of 61 RNA-Seq libraries from two different experiments (de-novo and transformed systems) are processed using the same pipeline for compatibility. The de-novo experiment consisted of 30 samples from three cell lines namely Lx110, Lx33, and Lx1322 where each cell line consists of five control replicates, and 5 Lurbinectedin treatment replicates. From this experiment, 16 samples were removed due to high variation between replicates, identified from PCA graphs. (3 from the Lx33 control group, 2 from the Lx33 treatment, 3 from the Lx110 control group, 2 from the Lx110 treatment group, 3 from the Lx1322 control group, 2 from the Lx1322 treatment group.) The transformed experiment consisted of 31 samples from two cell lines Lx831b and Lx1042, each with four conditions, Lurbinectedin treatment, Osimertinib treatment, combination treatment, and a vehicle control. All conditions had four replicates, except for the Lx1042 combination treatment, which had three replicates. From the transformed experiment, 12 samples were removed due to poor PCA clustering from high variation between replicates, one of which also had a unique alignment rate under 5% from the STAR aligner (1 from the Lx831b Lurbinectedin condition, 1 from the Lx831b Osimertinib condition, 2 from the Lx831b Vehicle group, 2 from the Lx831b Combination condition, 2 from the Lx1042 Lurbinectedin condition, 2 from the Lx1042 Vehicle group, 1 from the Lx1042 Osimertinib group, 1 from the Lx1042 combination group.) Quality control of raw reads has been performed using FastQC (v0.11.8). Trim Galore! (version 0.6.5) has been used to trim the adapter sequences with a quality threshold of 20

treatment_protocol: 1 million cells were injected in a 1:1 mixture of PBS and Matrigel in the flanks of NOD.Cg-Prkdc < scid > Il2rg < tm1Wjl > /SzJ (NSG) mice. After the initially development of mean tumor volume approximately 100 mm3, mice were randomized and treated with either vehicle (5% glucose+0.5%HPMC) or osimertinib (25 mg/kg. once a week) or lurbinectedin (0.2 mg/kg once a week) or combination of osimertinib and lurbinectedin (25 mg/kg. osimertinib with 0.2 mg/kg lurbinectedin once a week).

tag: model

value: in-vivo PDX model

value: Tumor tissue derived from lung

value: Human lung tumor tissue derived from patients

tag: recipient mouse


title: SCAT1_R1

value: Bone marrow stromal cells

value: Mesenchymal Stromal Cell

value: wt


title: PDX LX831b osimertinib+lurbinectedin_ rep.2

value: combination of osimertinib and lurbinectedin (25 mg/kg. osimertinib with 0.2 mg/kg lurbinectedin once a week).


title: PDX LX831b osimertinib+lurbinectedin_ rep.1


title: PDX LX831b osimertinib_ rep.3

value: osimertinib (25 mg/kg. once a week)


title: PDX LX831b osimertinib_ rep.4


title: PDX LX831b osimertinib_ rep.2


title: PDX LX831b lurbinectedin_ rep.4

value: lurbinectedin (0.2 mg/kg once a week)


title: PDX LX831b osimertinib_ rep.1


title: PDX LX831b lurbinectedin_ rep.2


title: 3hr_ST2_PMNpositive_2

description:
X3hr_ST2_PMNpositive_2
established from Whitlock-Witte type long-term bone marrow culture of BC8 mice

value: cell line

value: Bone marrow stromal cell

value: WT


title: PDX LX831b lurbinectedin_ rep.1


title: PDX LX831b lurbinectedin_ rep.3


title: PDX LX831b Control_ rep.4

value: vehicle (5% glucose+0.5%HPMC)


title: PDX LX831b Control_ rep.3


title: PDX LX831b Control_ rep.1


title: PDX LX831b Control_ rep.2


title: PDX LX1042 osimertinib+ lurbinectedin_ rep.3


title: PDX LX1042 osimertinib+lurbinectedin_ rep.2


title: PDX LX1042 osimertinib+lurbinectedin_ rep.1


title: PDX LX1042 osimertinib_ rep.4


title: PDX LX831b osimertinib+ lurbinectedin_ rep.3


title: PDX LX1042 osimertinib_ rep.1


title: PDX LX1042 lurbinectedin_ rep.3


title: PDX LX1042 lurbinectedin_ rep.2


title: PDX LX1042 lurbinectedin_ rep.4


title: PDX LX1042 Control_ rep.4


title: PDX LX1042 Control_ rep.3


title: PDX LX33-Lurbinectedin rep.5


title: PDX LX1042 Control_ rep.1


title: PDX LX33-Lurbinectedin rep.4


title: PDX LX33-Lurbinectedin rep.2


title: PDX LX33-Control rep.5


title: PDX LX33-Lurbinectedin rep.1


title: PDX LX33-Control rep.3


title: PDX LX33-Control rep.4


title: PDX LX33-Control rep.2


title: PDX LX1322-Lurbinectedin rep.4


title: PDX LX1322-Lurbinectedin rep.5


title: PDX LX33-Control rep.1


title: PDX LX1322-Lurbinectedin rep.3


title: PDX LX1042 osimertinib_ rep.3


title: PDX LX1042 osimertinib_ rep.2


title: PDX LX1322-Control rep.1


title: PDX LX1042 lurbinectedin_ rep.1


title: PDX LX1322-Control rep.2


title: PDX LX1322-Control rep.4


title: PDX LX110-Lurbinectedin rep.3


title: PDX LX110-Lurbinectedin rep.2


title: PDX LX1322-Control rep.3


title: PDX LX110-Lurbinectedin rep.5


title: PDX LX110-Lurbinectedin rep.4


title: PDX LX1042 Control_ rep.2


title: PDX LX110-Lurbinectedin rep.1


title: PDX LX33-Lurbinectedin rep.3


title: PDX LX110-Control rep.3


title: PDX LX110-Control rep.1


title: PDX LX110-Control rep.5


title: PDX LX1322-Lurbinectedin rep.2


title: PDX LX110-Control rep.2


title: PDX LX110-Control rep.4


title: hsp68 library in Crx-/- retina, biological replicate 3

status: Public on May 27 2023

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were written to file alongthe barcode's count. All other reads and barcodes were discarded.
Supplementary files format and content: First column contains unique 9 bp barcode, second column contains number of reads with the corresponding barcode.
Library strategy: Massively Parallel Reporter Assay

source_name: retinal explants

growth_protocol: All mouse lines were on the C57BL/6J background and free of rd1 and rd8 mutations. The CrxR90W/W, CrxR90W/+, CrxE168d2/d2and CrxE168d2/+ lines and their genotyping procedures were described by Tran et al. (PLoS Genetics 2014).

extract_protocol:
After culturing for 8 days retinas were placed in TRIzol (ThermoFisher) and RNA was extracted. Three replicate electroporations (6 retinas each) were performed.
cDNA was prepared using Superscript Reverse Transcriptase III (ThermoFisher) with oligo dT primers following the manufacturer’s instructions. Barcodes were amplified from cDNA or input plasmid DNA using 24 cycles of PCR with Phusion High Fidelity Master Mix (NEB). Amplicons were purified with the Monarch PCR kit (NEB), digested with MfeI-HF and SphI-HF (NEB) and ligated to custom sequencing adapters with PE2 indexing barcodes and phased P1 barcodes. Following 20 cycles of enrichment PCR, libraries were sequenced on the Illumina NextSeq platform to greater than 1000x coverage per sample.

treatment_protocol: Retinal explant electroporations were conducted as previously described by Kwasnieski et al. (PNAS 2012). Retinas were isolated from P0 mice and electroporated with 30 µg MPRA library and 30 µg pCAG-GFP as a transfection control.

value: retina

value: Crx -/-


title: hsp68 library in Crx-/- retina, biological replicate 1


title: hsp68 library in Crx-/- retina, biological replicate 2


title: hsp68 library in CrxE168d2/E168d2 retina, biological replicate 3


title: PDX LX1322-Control rep.5


title: PDX LX1322-Lurbinectedin rep.1


title: hsp68 library in CrxE168d2/E168d2 retina, biological replicate 2


title: hsp68 library in CrxR90W/R90W retina, biological replicate 2

value: Crx R90W/R90W


title: hsp68 library in CrxR90W/R90W retina, biological replicate 1


title: hsp68 library in CrxE168d2/E168d2 retina, biological replicate 1


title: hsp68 library in CrxR90W/R90W retina, biological replicate 3


title: hsp68 library in CrxE168d2/+ retina, biological replicate 2


title: hsp68 library in CrxE168d2/+ retina, biological replicate 1


title: hsp68 library in CrxR90W/+ retina, biological replicate 2

value: Crx R90W/+


title: hsp68 library in CrxE168d2/+ retina, biological replicate 3


title: hsp68 library in Crx+/+ retina, biological replicate 3

value: Crx +/+


title: hsp68 library in CrxR90W/+ retina, biological replicate 3


title: hsp68 library in Crx+/+ retina, biological replicate 1


title: hsp68 library in CrxR90W/+ retina, biological replicate 1


title: rho library in Crx-/- retina, biological replicate 3


title: rho library in Crx-/- retina, biological replicate 2


title: hsp68 library in Crx+/+ retina, biological replicate 2


title: rho library in Crx-/- retina, biological replicate 1


title: rho library in CrxE168d2/E168d2 retina, biological replicate 3


title: rho library in CrxE168d2/E168d2 retina, biological replicate 1


title: rho library in CrxR90W/R90W retina, biological replicate 3


title: rho library in CrxE168d2/+ retina, biological replicate 3


title: rho library in CrxR90W/R90W retina, biological replicate 2


title: rho library in CrxR90W/+ retina, biological replicate 3


title: rho library in CrxR90W/+ retina, biological replicate 2


title: rho library in CrxE168d2/+ retina, biological replicate 2


title: hsp68 plasmid library

description: Produced in E. coli DH5alpha

library_source: other

molecule: other

organism: synthetic construct

source_name: plasmid library


title: rho library in CrxE168d2/+ retina, biological replicate 1


title: rho plasmid library

description: Produced in E. coli DH5alpha


title: rho library in CrxR90W/+ retina, biological replicate 1


title: rho library in Crx+/+ retina, biological replicate 3


title: pooled_endMT_5

status: Public on May 03 2023

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

description:
10x Genomics
Lane 7 - ATAC

library_source: genomic

data_processing:
library strategy: multi-modal snRNA-seq and snATAC-seq
Alignement, filtering, barcode counting, peak calling, and counting of both ATAC and GEX molecules were made using the Cell Ranger ARC v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
BAM files (output from Cell Ranger ARC) for ATAC and gene expression were concatenated, sorted and indexed for demuxlet input BAM file using samtools (https://github.com/samtools/samtools)
Sample identity and identification of multiplets was performed for all samples and corresponding vcf and proccessed .bam files using demuxlet with --field set to "GT" (https://github.com/statgen/demuxlet)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

source_name: Ascending aorta

extract_protocol:
Nuclei from primary ECs were isolated according to 10x Genomics Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Demonstrated Protocol (CG000365, Rev C).
Library was performed according to 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (CG000338, v1).

value: Ascending aorta

value: Primary human aortic endothelial cells

value: Endothelial cells

value: 7d TGFB2 (10ng/mL), 7d IL1B (10ng/mL)


title: rho library in Crx+/+ retina, biological replicate 1


title: pooled_endMT_1

description:
10x Genomics
Lane 3 - ATAC

value: 7d ctrl, 7d siSCR


title: il1b6h

description:
10x Genomics
Lane 2 - ATAC

value: 6h IL1B (1ng/mL)


title: pooled_endMT_4

description:
10x Genomics
Lane 6 - ATAC

value: 7d ctrl, 4d siSCR, 7d TGFB2 (10ng/mL), 7d IL1B (10ng/mL)


title: rho library in CrxE168d2/E168d2 retina, biological replicate 2


title: pooled_endMT_2

description:
10x Genomics
Lane 4 - ATAC

value: 7d siRNA, 7d TGFB2 (10ng/mL), 4d TGFB2 (10ng/mL)


title: CC080_NRHV Sample 59

status: Public on Apr 25 2023

city: Chapel Hill

first: Timothy

middle: P

last: Sheahan

state: North Carolina

address: 3113 MHRC 135 Dauer Drive, Campus Box 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description:
CC080_NRHV
Tx w/ NRHV

data_processing:
FastQ file quality was assessed using FastQC and MultiQC.
FastQ reads were mapped and quantified using Kallisto (0.46.1) to the reference "GRCm39 GENCODE VM27".
Counts per million (CPM) was calculated and normalized using EdgeR (3.38.4), keeping only rows with at least 5 cells indicating a count-per-million (CPM) of at least 1.
Expression data was filtered and normalized using Limma's (3.52.4) VOOM.
Differentially expressed genes (DEGs), identified by a log-fold change >= 1.5 or <= 1.5 with an adj.p.val of <.05, were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: version 27 of mouse reference genome GRCm39
Supplementary files format and content: comma seperated value file that includes log2 counts per million (CPM) values for each Sample

source_name: CC080 Mouse

growth_protocol: Mice were housed at UNC Chapel Hill and received standard mouse chow

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the Kapa mRNA Stranded according to the manufacturer’s instructions.
RNA-seq. Run on a HiSeq 4000 (HS), Single end, 1x50.

treatment_protocol: Mice were humanely sacrificed, liver tissue was removed and stored in RNAlater at -80C until processing.

tag: background strain

value: NRHV


title: CC080_NRHV Sample 52

description:
CC080_NRHV
Tx w/ NRHV


title: CC080_NRHV Sample 53

description:
CC080_NRHV
Tx w/ NRHV


title: CC080_PBS Sample 51

description:
CC080_PBS
Tx w/ PBS

value: PBS


title: CC080_PBS Sample 49

description:
CC080_PBS
Tx w/ PBS


title: rho library in CrxR90W/R90W retina, biological replicate 1


title: CC080_PBS Sample 50

description:
CC080_PBS
Tx w/ PBS


title: CC071_NRHV Sample 38

description:
CC071_NRHV
Tx w/ NHRV

source_name: CC071 Mouse

value: NHRV


title: CC071_NRHV Sample 37

description:
CC071_NRHV
Tx w/ NHRV


title: CC071_PBS Sample 31

description:
CC071_PBS
Tx w/ PBS


title: CC046_NHRV Sample 23

description:
CC046_NHRV
Tx w/ NRHV

source_name: CC046 Mouse


title: CC046_NHRV Sample 27

description:
CC046_NHRV
Tx w/ NRHV


title: U-251MG rep 2 [P189_144]

source_name: Brain

value: Brain

value: WT


title: CC046_PBS Sample 19

description:
CC046_PBS
Tx w/ PBS


title: pooled_endMT_3

description:
10x Genomics
Lane 5 - ATAC


title: CC071_PBS Sample 32

description:
CC071_PBS
Tx w/ PBS


title: B6_PBS Sample 15

description:
B6_PBS
Tx w/ PBS

source_name: C57BL/6 Mouse


title: B6_PBS Sample 16

description:
B6_PBS
Tx w/ PBS


title: ctrl6h

description:
10x Genomics
Lane 1 - ATAC

value: 6h control media


title: B6_PBS Sample 14

description:
B6_PBS
Tx w/ PBS


title: CC046_PBS Sample 17

description:
CC046_PBS
Tx w/ PBS


title: rho library in Crx+/+ retina, biological replicate 2

value: retina


title: B6_NRHV Sample 5

description:
B6_NRHV
Tx w/ NRHV


title: B6_NRHV Sample 7

description:
B6_NRHV
Tx w/ NRHV


title: B6_NRHV Sample 4

description:
B6_NRHV
Tx w/ NRHV


title: Ae. albopictus Suscepible Sebring colony tech rep 4

status: Public on Feb 28 2023

city: College Station

first: Xinyue

last: Huang

address: 300 Spruce street, Apt 303

department: Entomology

institute: Texas A&M University

data_processing:
Genome Analysis Toolkit (GATK) Best Practices for RNA sequencing data
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (version 0.6.4_dev)
Trimmed sequence reads were mapped to Aedes albopictus reference genome (downloaded from VectorBase, version CpipJ2.4) using STAR (version 2.7.3a)
Picard tools (version 2.20.1) was used to identify and add Read Group (RG) for BAM files obtained from two-pass alignment. Next, reads were counted using featureCounts (version 1.6.0).
Assembly: CpipJ2.4
Supplementary files format and content: tab-delimited text files include raw count value generated from featureCounts for each sample

organism: Aedes albopictus

source_name: Total tissue

extract_protocol:
Extract protocol used was developed for fatty tissues using QIAzol Lysis Reagent. RNA products were purified with the QIAGEN® RNeasy Mini Kit.
RNA libraries for RNA-seq were prepared using PerkinElmer NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 following manufacturer's protocols.

treatment_protocol: Malathion resistant group and malathion susceptible groups were exposed to malathion at a concentration of 400 μg/bottle for 120 min with CDC standard bottle bioassay following instructions in the CONUS manual.

value: Total tissue

tag: sample group

value: Suscepible Sebring colony

tag: sample status

value: From laboratory susceptible Sebring strain

value: laboratory susceptible Sebring strain


title: Ae. albopictus Suscepible Sebring colony tech rep 3


title: Ae. albopictus Suscepible Sebring colony tech rep 5


title: CC071_PBS Sample 33

description:
CC071_PBS
Tx w/ PBS


title: B6_PBS Sample 13

description:
B6_PBS
Tx w/ PBS


title: Ae. albopictus Wild collected group tech rep 4

value: Wild collected group

value: WT not treated with bottle assay


title: Ae. albopictus Wild collected group tech rep 5


title: Ae. albopictus Suscepible Sebring colony tech rep 1


title: CC046_NHRV Sample 24

description:
CC046_NHRV
Tx w/ NRHV


title: CC046_PBS Sample 18

description:
CC046_PBS
Tx w/ PBS


title: Ae. albopictus Wild collected group tech rep 2


title: Ae. albopictus Malthion susceptible tech rep 5

value: Malthion susceptible

value: Knockdown during bottle assay

value: malathion exposure using CDC bottle assay


title: Ae. albopictus Malthion susceptible tech rep 2


title: Ae. albopictus Wild collected group tech rep 1


title: Ae. albopictus Malthion susceptible tech rep 3


title: Ae. albopictus Malthion susceptible tech rep 4


title: Ae. albopictus Malthion susceptible tech rep 1


title: Ae. albopictus Malathion resistant tech rep 5

value: Malathion resistant

value: Alive after bottle assay


title: Ae. albopictus Malathion resistant tech rep 4


title: Ae. albopictus Malathion resistant tech rep 3


title: Ae. albopictus Malathion resistant tech rep 1


title: B6_NRHV Sample 6

description:
B6_NRHV
Tx w/ NRHV

value: NRHV


title: Ae. albopictus Malathion resistant tech rep 2


title: Ae. albopictus Suscepible Sebring colony tech rep 2


title: POD_liver_spatial_048h_C

status: Public on Feb 01 2023

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Demultiplexing, alignment (to the mm10 reference), orientation to tissue slide, and estimation of cell-containing partitions and associated UMIs using Space Ranger 1.0.0.
Quality control, normalisation, data integration, and downstream analysis using Seurat 4.1.1.
Assembly: mm10 (Ensembl 93)
Supplementary files format and content:
mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample; tif: tissue slide image per sample
png, jpg: tissue slide images; json: scale factors for images; csv: tissue positions for images

source_name: Liver

extract_protocol:
Samples were snap-frozen on dry ice and cryogenic-sectioned at 10um, then placed on spatial gene expression slides.
10x Genomics spatial 3’ gene expression v1
OTHER: spatial transcriptomics (10x)

value: Liver

tag: disease

value: POD


title: POD_liver_spatial_048h_D

description: 10x Genomics spatial 3’ gene expression v1


title: Ae. albopictus Wild collected group tech rep 3

value: WT


title: POD_liver_spatial_048h_A


title: POD_liver_spatial_024h_B


title: Healthy_liver_spatial_003

value: Uninjured


title: POD_liver_spatial_036h_B


title: Healthy_liver_spatial_004


title: POD_liver_spatial_024h_A


title: NonAE_liver_spatial_05

description: 10x Genomics spatial 3' gene expression v1

data_processing:
Demultiplexing, alignment (to the GRCh38 reference), orientation to tissue slide, and estimation of cell-containing partitions and associated UMIs using Space Ranger 1.0.0.
Quality control, normalisation, data integration, and downstream analysis using Seurat 4.1.1.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content:
mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample; tif: tissue slide image per sample
png, jpg: tissue slide images; json: scale factors for images; csv: tissue positions for images

source_name: NonAE liver explant

value: NonAE liver explant


title: NonAE_liver_spatial_03


title: Healthy_liver_spatial_02

source_name: Healthy liver explant

value: Healthy liver explant


title: Healthy_liver_spatial_01


title: POD_liver_spatial_048h_B


title: Healthy_liver_spatial_10


title: APAP_liver_spatial_01_B

source_name: APAP liver explant

value: APAP liver explant


title: POD_liver_spatial_036h_A


title: 210322_TFmap_S23

status: Public on Jan 05 2023

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

description:
TF mapping results for 210322_TFAtlas_S23
library strategy: amplicon

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by SHARE-seq pipeline (csv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)

source_name: H1 human embryonic stem cells

extract_protocol:
RNA was extracted using SHARE-seq
single-cell RNA-Seq libraries were prepared using SHARE-seq. Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation

tag: cell type

value: H1 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 897 transcription factors

tag: time point

value: 7 days


title: 210322_TFmap_S22

description:
TF mapping results for 210322_TFAtlas_S22
library strategy: amplicon


title: APAP_liver_spatial_03


title: APAP_liver_spatial_01_A


title: INPUT-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3

status: Public on Dec 28 2022

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: CTCFAID2/WT cells treated with Triptolide

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina)
Raw reads were first trimmed using TrimGalore (v0.6.3). Filtered reads are then aligned the Homo sapiens reference genome GRCm37.p13 using BWA (v0.7.17-r1198). Duplicated reads are then marked using the “bamsormadup” function from the biobambam2 tool (v2.0.87)
PCR duplicates and low mapping quality reads (MAPQ < 1) were removed using samtools (version 1.9, parameter ‘-q 1 -F 1024’).
The uniquely mapped reads were then used to estimate the average fragment length in each sample based on the cross-correlation profile calculated from SPP (v1.11) [PMID:19029915]. The smallest fragment size estimated by SPP was used to center and extend reads to generate bigwig files. The bigiwig signal in all samples is  scaled to 15 million reads (ie: scaling-factor=15e6/libSize). Macs2 (v 2.1.1) was used to call peaks using parameters “-g hs  --nomodel --extsize <SPP_fragmentSize>”. Two sets of peaks were generated: Strong peaks called with parameter ‘-q 0.05’ and weak peaks called with parameter ‘-q 0.5’. Peaks were considered reproducible if they were supported by a strong peak from each replicate or at least one strong peak and a weak peak
Assembly: hg19
Supplementary files format and content: bw

source_name: cell line

growth_protocol: CTCFAID2 cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol: 20million cells were fixed for 5mins with 1% formaldehyde.  Covaris truChIP chromatin shearing kit was used to prepare chromatin.  Spike-in control was included (Active Motif). Chromatin was incubated overnight with 10ug CTCF antibody (Diagenode). 50ul Protein G dynabeads were added and incubated for 4hrs at 4oC.  For HA tagged samples, spike in was not included.  Sheared chromatin was incubated for 4hrs with  25ul Anti-HA magnetic beads (Pierce).  For all samples, after washing DNA was decrosslinked and eluted in TE+1%SDS, Proteinase K, 400uM NaCl.  DNA was purified by phenol cholorform isoamyl alcohol.

treatment_protocol: CTCFAID2 cells were treated with 10uM 5-Ph-IAA (Med Chem Express). For cells with HA tagged CTCFs, 1ug/ml doxycycline was added to induce expression.

value: SEM

tag: antibody

value: none (input)

tag: treatment

value: Triptolide


title: Healthy_liver_spatial_002

tag: tissue


title: INPUT-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2


title: INPUT-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1


title: INPUT-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3

description: CTCFAID2/WT cells treated with RNase A

value: RnaseA


title: 210322_TFmap_S24

description:
TF mapping results for 210322_TFAtlas_S24
library strategy: amplicon


title: INPUT-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2

description: CTCFAID2/WT cells treated with RNase A


title: INPUT-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3

description: CTCFAID2/WT cells treated with DMSO

value: DMSO


title: INPUT-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1

description: CTCFAID2/WT cells treated with RNase A


title: INPUT-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2

description: CTCFAID2/WT cells treated with DMSO


title: INPUT-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1

description: CTCFAID2/WT cells treated with DMSO


title: CTCF-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2

value: CTCF


title: CTCF-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3


title: CTCF-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3

description: CTCFAID2/WT cells treated with RNase A


title: CTCF-Trip_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1


title: CTCF-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R3

description: CTCFAID2/WT cells treated with DMSO


title: CTCF-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2

description: CTCFAID2/WT cells treated with RNase A


title: CTCF-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R2

description: CTCFAID2/WT cells treated with DMSO


title: CTCF-DMSO_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1

description: CTCFAID2/WT cells treated with DMSO


title: 210322_TFmap_S21

description:
TF mapping results for 210322_TFAtlas_S21
library strategy: amplicon


title: knockout rep6 [FB84]

status: Public on Nov 18 2022

city: BOSTON

first: CHANG

last: CAO

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Reads were trimmed by trimmomatic v0.36 and high-quality reads were aligned to mouse reference genome (GRCm38.p6) using STAR 2.5.2b.
The reads counts were calculated by featureCounts software from the Subread package v1.5.2.
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: placenta

extract_protocol:
RNA was extracted from placenta using Rneasy plus mini kit (Qiagen, cat. no. 73404).
NEBNext Ultra RNA Library Prep Kit for Illumina (cat. no. E7770) was used for the construction of sequencing libraries following manufacturer’s instructions.

value: placenta

tag: genotype

value: knockout

tag: Sex

value: male

tag: time

value: Embryonic day 15.5


title: control rep4 [FB81]

tag: strain

value: control


title: control rep3 [FB59]


title: control rep2 [FB55]


title: control rep1 [FB29]


title: knockout rep3 [FB49]


title: knockout rep4 [FB57]


title: knockout rep5 [FB82]


title: knockout rep1 [FB32]


title: B16, day 10, mouse 1, rep D1 and D2, experiment 1

status: Public on Nov 01 2022

first: Anna

last: Lyubetskaya

address: 100 Binney St

institute: Bristol-Myers Squibb

description:
Illumina NextSeq 550
Visium ST library
Please note that SRR21177768 does not contain the file B16_d10_m1_D1-D2_e1_R2_001.fastq.gz. This file was unreadable and could not be loaded at SRA.

data_processing:
All sequencing outputs were processed using SpaceRanger-1.2.1 (10x Genomics) with rat (Rnor6.0ERCC-ensembl98), mouse (mm10-2020-A), and human (GRCh38-2020-A) references.
Assembly: Rnor6.0ERCC-ensembl98, mm10-2020-A, GRCh38-2020-A
Supplementary files format and content: 10x Genomics SpaceRanger output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, scalefactors_json.json, tissue_hires_image.png, tissue_positions_list.csv
Supplementary files format and content: Full scale TIFF images
Library strategy: ST RNAseq (Visium and Visium for FFPE)

source_name: B16F10 syngeneic tumor

growth_protocol: B16F10 and MC38 mouse tumor samples were grown by subcutaneous implantation of 1e6 or 1.5e6 B16F10 or MC38 cells, respectively, into the flank of female C57BL/6 mice. Tumors were harvested 10 days (d10) or 16 days (d16) post-implantation.

extract_protocol:
Rat colons were collected from 6-8 week-old Sprague-Dawley rats and were rinsed with ice-cold PBS before O.C.T. or FFPE embedding. Mouse syngeneic tumors were collected in ice-cold PBS before O.C.T. embedding. O.C.T. embedding was accomplished by placing tissue in a cryomold with ice-cold TissueTek O.C.T. Compound on an aluminum block pre-cooled in a dry ice ethanol bath. FFPE tissues were first placed in 10% neutral buffered formalin for 24-hour fixation, after which tissue was processed for embedding in a Sakura VIP automated system with vacuum/pressue cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning.  All tumor resection smples were obtained with informed concesnt from BioIVT and Discovery Life Sciences. The Donor-A tumor (BioIVT) was divided prior to fixation, one half was O.C.T. embedded, the other half was FFPE embedded.
All mouse B16F10 and MC38 samples, and fresh-frozen (FF) rat colon and Donor-A PDAC samples were processed with the Visium Spatial Gene Expression kit (10X Genomics, PN-1000184) according to manufacturer protocol (10X Genomics, CG000160 Rev A and CG000238 Rev D for sectioning/staining and library preparation, respecitvely). Rat colon FF samples with a coverslip (wCS) were coverslipped during imaging, according to manufacturer protocol (10X Genomics, CG000160 RevA). Rat colon and Donor-A FFPE polyA-capture (FFPE-pA) samples were processed as described in Villacampa, et al., Cell Genomics 2021, using reagents from the Visium Spatial gene Expression kit (10X Genomics, PN-1000184), with a modified permeabilization, using 2X permeabilization enzyme for 60 minutes (permebailization enzyme was dissovled at 4 mg/ml (4X) in 0.1 N HCl and diluted to 2X in 0.1 N HCl). Donor A-C FFPE probe samples (FFPE-probes) were processed according to the Visium FFPE Regeant kit with Human Transcriptome Probe kit (10X Genomics, PN-100362 and PN-1000364) according to manufacturer protocol (10X Genomics, CG000409 Rev A and CG000407 Rev A for sectioning/staining and library preparation, respectively).

value: B16F10 syngeneic tumor


title: CTCF-RnaseA_4hrs_TRE3G-WT-HA_5PhIAA_Dox_R1

description: CTCFAID2/WT cells treated with RNase A


title: episuppressor_3-75-WGBS

status: Public on Oct 24 2022

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: genomic DNA

data_processing:
Whole genome Seq: sickle se -f -t sanger -o; bowtie -l 50 -n 3 --best -p 1; samtools view -bS -o; samtools sort; samtools mpileup -uf; bcftools view -bvcg
Whole Genome Bisulfite Seq: bismark; bismark_methylation_extractor -p --bedGraph --no_overlap --report --CX --counts --cytosine_report  -  genome_folder
Genome_build: A.thaliana (tair10)
Supplementary_files_format_and_content: DNA-seq: text files are lists of mutations; Whole Genome Bisulfite Seguencing: bedGraph are rate of methylated aligned reads.

organism: Arabidopsis thaliana

source_name: rossette leaves

growth_protocol: grown on soil

extract_protocol:
Nucleon DNA extraction kit
Illumina Whole Genome Bisulfite Seq library prep as described in Creasey et al., 2014

value: 4 week old rossette leaves 1g

value: rdr1 rdr2 rdr6 ddm1

tag: ecotype

value: Columbia

tag: illumina platform

tag: read type


title: episuppressor_3-72-WGBS

description: genomic DNA


title: rdr1rdr2rdr6ddm1-WGBS

description: genomic DNA


title: episuppressor_2-69-WGBS

description: genomic DNA


title: episuppressor_3-75-WGS

description: genomic DNA

data_processing:
Library strategy: DNA-seq
Whole genome Seq: sickle se -f -t sanger -o; bowtie -l 50 -n 3 --best -p 1; samtools view -bS -o; samtools sort; samtools mpileup -uf; bcftools view -bvcg
Whole Genome Bisulfite Seq: bismark; bismark_methylation_extractor -p --bedGraph --no_overlap --report --CX --counts --cytosine_report  -  genome_folder
Genome_build: A.thaliana (tair10)
Supplementary_files_format_and_content: DNA-seq: text files are lists of mutations; Whole Genome Bisulfite Seguencing: bedGraph are rate of methylated aligned reads.

extract_protocol:
Nucleon DNA extraction kit
Illumina DNAseq library prep


title: rdr1rdr2rdr6-WGBS

description: genomic DNA


title: episuppressor_2-20-WGBS

description: genomic DNA


title: rdr1rdr2rdr6ddm1-WGBS-2

description: genomic DNA


title: episuppressor_3-72-WGS

description: genomic DNA


title: episuppressor_2-20-WGS

description: genomic DNA


title: rdr1rdr2rdr6-WGS

description: genomic DNA

value: rdr1 rdr2 rdr6


title: epiRL_stertile10

description: genomic DNA

value: rdr1 rdr2 rdr6, ddm1epiRL


title: epiRL_stertile9

description: genomic DNA


title: epiRL_stertile7

description: genomic DNA


title: epiRL_stertile6

description: genomic DNA


title: knockout rep2 [FB48]


title: epiRL_stertile5

description: genomic DNA


title: epiRL_stertile4

description: genomic DNA


title: epiRL_stertile3

description: genomic DNA


title: epiRL_stertile2

description: genomic DNA


title: rdr1rdr2ddm1-WGBS

description: genomic DNA

value: rdr1 rdr2 ddm1


title: epiRL_stertile1

description: genomic DNA


title: epiRL_fertile10

description: genomic DNA


title: epiRL_fertile7

description: genomic DNA


title: epiRL_fertile9

description: genomic DNA


title: epiRL_fertile8

description: genomic DNA


title: epiRL_fertile6

description: genomic DNA


title: episuppressor_2-69-WGS

description: genomic DNA


title: epiRL_fertile5

description: genomic DNA


title: epiRL_fertile2

description: genomic DNA


title: epiRL_stertile8

description: genomic DNA


title: epiRL_fertile3

description: genomic DNA


title: D50_3D_rep1

status: Public on Oct 18 2022

city: Brno

first: Ece

last: Ergir

address: Studentska 6

department: Center for Translational Medicine (CTM)

country: Czech Republic

institute: St. Anne´s University Hospital Brno - International Clinical Research Centre (FNUSA-ICRC)

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
6-nt long UMIs were extracted and subseqeuntly used for deduplication of aligned reads by UMI-tools v. 1.1.1.
6-nt long barcode sequence related to Lexogen QuantSeq Library Prep Kit were trimmed using seqtk 1.3-r106, the adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using featureCounts tool v1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample gathered by featureCounts tool
Supplementary files format and content: Resulting table based on the analysis of differential gene expression performed by DESeq2 tool containing foldchanges and related statistics supplied with matrix with normalized counts for every gene and every sample

source_name: 3D microtissue (hOCMT) - hiPSC derived

growth_protocol: hiPSC culture an maintenance was described previously by Pagliari et al (1). Cardiac differentiation was achieved by using the human iPSC cell line DF 19–9-7 T (iPS, karyotype: 46, XY) was purchased from WiCell (Madison, WI, USA), and was  performed following the Wnt signalling modulation protocol by Lian et.al. (2,3), with slight modifications as previously described by Pagliari et al (1). Briefly, prior to cardiovascular differentiation, hiPSCs were dissociated into single cells (TrypLE Select, Thermo Fisher Scientific) and re-seeded onto 12-well Matrigel-coated plates with 2.0 × 10^5 cells/cm2, with complete Essential 8 medium including Y27632 Rock Inhibitor (RI) (1:4000 dilution from 10 μM stock, 2.5 μM final, Selleck chemicals, Houston, TX, USA). The next day, the medium was replaced with complete Essential 8 medium without RI, and the medium exchange was performed daily until the cells reached 100% confluency. On day 0, to start mesoderm differentiation, the medium was changed with RPMI 1640 with L-Glutamine (Biosera) media supplemented with P/S, B-27™ supplement minus insulin (1×, Thermo Fisher Scientific) and CHIR99021 (8 µM, Sigma-Aldrich). On day 2, the medium was exchanged with RPMI 1640+B-27 minus insulin (RPMI+B27-Ins), supplemented with IWP-2 (5 µM, Selleck chemicals). On day 4, the medium was replaced with RPMI+B27-Ins, and medium exchange was performed every 2 days until the cells started beating (usually on day 7, but may depend on the iPSC line). Once beating clusters started to emerge, the medium was replaced with RPMI 1640+B-27™ supplement (RPMI+B27+Ins) (1×, Thermo Fisher Scientific), and medium exchange was performed every 2-3 days until day 15 of differentiation. From day 15 on, the cells were used either for generation of 3D hOCMTs, or were continued to be cultured as 2D monolayers as controls, with medium exchange every 3-4 days until the end of experiments, on day 30 or day 50 endpoints.    REFERENCES:  1. Pagliari, S. et al. YAP–TEAD1 control of cytoskeleton dynamics and intracellular tension guides human pluripotent stem cell mesoderm specification. Cell Death Differ. 2020 284 28, 1193–1207 (2020).  2. Lian, X. et al. Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling. Proc. Natl. Acad. Sci. U. S. A. 109, E1848–E1857 (2012).  3. Lian, X. et al. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nat. Protoc. 8, 162–175 (2013).

extract_protocol:
For RNA isolation, 3D microtissue and 2D controls were dissociated by using MACS MultiTissue Dissociation Kit 3 on day 30 and day 50. After cell dissociation, RNA was extracted with High Pure RNA Isolation Kit (Roche) according to manufacturer’s instructions, and quantified with Nanodrop 2000 Spectrophotometer (Thermo Fisher Scientific). Quality control for RNA integrity number (RIN) was also determined with Agilent 2100 Bioanalyzer.
500 nanograms of total RNA per sample was used as an input for library preparation using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Briefly, RNA was transcribed into cDNA using oligodT primer (FS1) at half volume compared to the manufacturer's instructions to minimize the off-target products. Following the first strand synthesis, RNA removal and second strand synthesis were performed using the UMI Second Strand Synthesis Mix (USS) containing Unique Molecular Identifiers (UMIs) that allow detection and removal of PCR duplicates. Finally, sequencing libraries were created by PCR with i5 Unique Dual Indexing Add-on Kit for Illumina (Lexogen). The quality and quantity of libraries was determined using Fragment Analyzer by DNF-474 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and QuantiFluor dsDNA System (Promega). Final library pool was sequenced on Illumina NextSeq 500 with 75 bp single-ends

tag: time-point

value: Day 50

tag: strain origin

value: iPSC DF 19-9-7 (karyotype:46, XY, WiCell)


title: D30_3D_rep2

value: Day 30


title: epiRL_fertile1

description: genomic DNA


title: epiRL_fertile4

description: genomic DNA


title: S56A

status: Public on Aug 02 2022

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description: R1 fastq file: cDNA; R2 fastq file: barcode/UMI

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCm38
Supplementary files format and content: tab-delimited text file containing raw read count values per gene for each sample

source_name: Pancreatic ductal adenocarcinoma cells

extract_protocol:
Qiagen RNeasy Plus Micro Kit
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.

tag: batch

tag: replicate

tag: dimension

tag: environment

value: collagen

tag: day

value: KPC


title: D50_3D_rep3


title: D30_3D_rep1


title: S56C


title: S38B

value: KC


title: S56B


title: D30_3D_rep3


title: S55-9591-bulk3D13D-17D


title: S38A


title: S54-9591-bulk3D13D-17C


title: S53-9591-bulk3D13D-17B


title: D50_3D_rep2


title: S52-9591-bulk3D13D-17A


title: S50-9591-bulk3D7D-16B


title: S48-9591-matrigel3D-15C

value: matrigel


title: S38C


title: S49-9591-bulk3D7D-16A


title: S46-9591-matrigel3D-15A


title: S51-9591-bulk3D7D-16C


title: S47-9591-matrigel3D-15B


title: S45-9591-2D-14F


title: S44-9591-2D-14E


title: S43-9591-2D-14D


title: S42-9591-2D-14C


title: S56-9591-bulk3D13D-17E


title: S40-9591-2D-14A


title: Tumor-26

status: Public on Jun 01 2022

city: Tampa

first: Dennis

last: Adeegbe

state: FL

address: 13131 USF Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center

data_processing:
10x Genomics Cell Ranger (version 3.0.2) vdj pipeline was used for demultiplexing, barcode processing, sequence assembly, and paired clonotype calling.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Assembly: GRCH38
Supplementary files format and content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell

extract_protocol:
Single-cell TCR-sequencing was performed using the 10X Genomics Chromium system. Single cells, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs) and then reverse transcription of poly-adenylated mRNA was performed inside each droplet
The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 5’ v1.1 and V(D)J Reagent Kits.
5,000 sequencing reads per cell for VDJ libraries were generated on the Illumina NextSeq 500 instrument.

treatment_protocol: Melanoma-bearing mice were treated with anti-CD25 or Rat IgG isotype antibody 2x/week beginning from day 7 post tumor inoculation and up to day 21.

value: B16-F10 Melanoma


title: Tumor-31


title: Tumor02


title: Tumor-33


title: Spleen03-VDJ


title: Spleen01-VDJ


title: Spleen02-VDJ


title: B16-F10-06-Tumor-VDJ


title: Spleen-69


title: Tumor03


title: Tumor01


title: Spleen-27


title: B16-F10-01-Tumor-VDJ


title: Spleen-26


title: B16-F10-09-Tumor-VDJ


title: B16-F10-03-Tumor-VDJ


title: SCI_Brg1-031621-2

status: Public on May 26 2022

city: Los Angeles

first: Joshua

middle: Evan

last: Burda

address: 127 S San Vicente Blvd

department: Biomedical Sciences, Center for Neural Science and Medicine

institute: Cedars Sinai Medical Center

description: SCI SMARCA4cKO

data_processing:
genome alignment: cellranger-ATAC-v1.2
peak-calling: MACS2-v.2.27.1
data normalization and clustering: ArchR- v1.0.1
Assembly: mm10
Supplementary files format and content: .h5, ATAC peaks per cell

source_name: thoracic spinal cord

extract_protocol:
Fourteen days after complete crush SCI, spinal cords of wild-type, Stat3-astro-cKO or Smarca4-astro-cKO mice were perfused with ice cold saline and spinal cords rapidly dissected and frozen on dry ice. For SCI samples, the central 3 mm of the lower thoracic lesion including the lesion core and 1 mm rostral and caudal were then rapidly removed and snap frozen in liquid nitrogen. Anatomically equivalent regions of spinal cord were taken from healthy controls. Frozen tissue samples were processed for immunoprecipitation of astrocyte nuclei for snATACseq. Astrocyte nuclei were isolated by antibody-binding and magnet-assisted nuclear immunoprecipitation (MAN-IP) using well characterized procedures. In breif, tissues were dissociated and single nuclei suspensions were incubated with Sox9 rabbit monoclonal antibody to positively select for astrocyt nuclei by MAN-IP.
Single nuclei partitioning, barcoding and library preparation was performed using the 10X Genomics Chromium Controller and Chromium™ Single Cell ATAC Solution, and sequenced using Novaseq S2 (illumina).
Libraries were prepared per the protocol for the 10x Genomics Single Cell ATAC Solution

value: Crush SCI at T10


title: SCI_Stat3-031921-2

description: SCI STAT3cKO


title: SCI_Stat3-031921-1

description: SCI STAT3cKO


title: B16-F10-05-Tumor-VDJ


title: SCI_WT-031221-2

description: SCI WT


title: SCI_WT-031221-1

description: SCI WT


title: S41-9591-2D-14B


title: SCI_Brg1-031621-1

description: SCI SMARCA4cKO


title: NO_SCI_WT_CON-030921-2

description: No SCI Control, WT


title: NO_SCI_WT_CON-030921-1

description: No SCI Control, WT


title: LPS_WT_012621-2 (was LPS CTL)

extract_protocol:
Twenty fours hours following IP injection of LPS, spinal cords of wild-type, Stat3-astro-cKO or Smarca4-astro-cKO mice were perfused with ice cold saline and spinal cords rapidly dissected and frozen on dry ice. 3 mm of the lower thoracic spinal cord was then rapidly removed and snap frozen in liquid nitrogen. Anatomically equivalent regions of spinal cord were taken from healthy controls. Frozen tissue samples were processed for immunoprecipitation of astrocyte nuclei for snATACseq. Astrocyte nuclei were isolated by antibody-binding and magnet-assisted nuclear immunoprecipitation (MAN-IP) using well characterized procedures. In breif, tissues were dissociated and single nuclei suspensions were incubated with Sox9 rabbit monoclonal antibody to positively select for astrocyt nuclei by MAN-IP.
Single nuclei partitioning, barcoding and library preparation was performed using the 10X Genomics Chromium Controller and Chromium™ Single Cell ATAC Solution, and sequenced using Novaseq S2 (illumina).
Libraries were prepared per the protocol for the 10x Genomics Single Cell ATAC Solution

value: Intraperitoneal LPS injection

tag: condition

value: LPS WT

value: thoracic spinal cord


title: LPS_WT_012621-1 (was LPS CTL)

tag: treatment


title: LPS_STAT3_012621-2

value: LPS STAT3cKO

tag: tissue


title: LPS_BRG1_012621-1

tag: genotype

value: LPS SMARCA4cKO


title: LPS_BRG1_012621-2


title: NO_LPS_SC-CON-020221-2

value: No LPS Control, WT


title: NO_LPS_SC-CON-020221-1


title: 8188 HA

description: DEA_refSeq_WT_LPS_vs_WT_Uninj_Complete_geneList_EdgeR

data_processing:
genome alignment: STAR aligner (v.2.4.0j)
Read counting: HT-seq (v.0.6.0)
data normalization and differential expression: EdgeR (v.3.28.0)
Assembly: mm10
Supplementary files format and content: xlsx; Gene ID; Log2FC; raw and normalized read counts

extract_protocol:
Astrocyte ribosome-associated mRNA isolation: Fourteen days after complete crush SCI or 24 hours following IP injection of LPS, spinal cords of wild-type, Stat3-astro-cKO or Smarca4-astro-cKO mice were perfused with ice cold saline and spinal cords rapidly dissected and frozen on dry ice. For SCI samples, the central 3 mm of the lower thoracic lesion including the lesion core and 1 mm rostral and caudal were then rapidly removed and snap frozen in liquid nitrogen. Anatomically equivalent regions of spinal cord were taken from mice treated with LPS or from genotype-matched healthy controls. Frozen tissue samples were processed either for RiboTag analysis via haemagglutinin (HA) immunoprecipitation and purification of astrocyte ribosome-associated mRNA using standard methods.
Astrocyte RNA Integrity was analysed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip, RIN ≥ 8.9 for all samples. cDNA was generated from 10 ng of RNA using the Universal plus mRNA-Seq Kit (Nugen).
Multiplexed sequencing was performed with a NovaSeq 6000 sequencer (Illumina) on a NovaSeq S2 flow cell to produce 50 base-pair paired-end reads.


title: 8091 HA


title: 8090 HA


title: 8089 HA


title: 7345 HA


title: 7337 HA


title: 7341 HA


title: 7118 HA


title: 8009 HA

description: DEA_refSeq_STAT3cKO_LPS_vs_STAT3cKO_Uninj_Complete_geneList_EdgeR


title: 7961 HA


title: 7981 HA


title: 7141 HA


title: 7142 HA


title: 7788 HA


title: 7966 HA

description: DEA_refSeq_SMARCA4cKO_SCI_vs_SMARCA4cKO_Uninj_Complete_geneList_EdgeR


title: 7139 HA


title: 8200 HA


title: 7996 HA

description: DEA_refSeq_SMARCA4cKO_LPS_vs_SMARCA4cKO_Uninj_Complete_geneList_EdgeR


title: 8060 HA


title: 7979 HA


title: 7817 HA

description: DEA_refSeq_SMARCA4cKO_LPS_vs_SMARCA4cKO_Uninj_Complete_geneList_EdgeR, DEA_refSeq_SMARCA4cKO_SCI_vs_SMARCA4cKO_Uninj_Complete_geneList_EdgeR


title: 8108 HA


title: 8063 HA


title: LPS_STAT3_012621-1


title: 8109 HA