title: Col-0, D33, FT, LDSD, EM-seq, chamber B>A

city: Berkeley

first: Dawei

last: Dai

address: 2151 Berkeley Way

institute: University of California, Berkeley

description:
Library name: Col-0_D33_FT_LDSD__chamber_B_A
150x 150

data_processing:
Reads were preprocessed with TrimGalore 0.6.6 (Babraham Bioinformatics) to remove adaptors
Bismark 0.22.3 (2) was used to map filtered reads to the A. thaliana TAIR10 genome, allowing for 0 mismatch per read in the seed region and removing PCR duplicates.
Methylation values for each cytosine were calculated as #C/(#C+#T) using the Bismark methylation extractor function.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited bed files includes methylation level at single base resolution in CHH, CHG, and CG context for each sample.
Library strategy: EM-seq

organism: Arabidopsis thaliana

source_name: First true leaves

extract_protocol:
DNA was isolated using the CTAB method.
EM-seq libraries were constructed following the NEBNext® Enzymatic Methyl-seq Kit protocol with 50 ng initial DNA (25 ng for all embryo samples). Library quality was verified with a KAPA Library Quant Kit and fragment analyzer. Libraries were pooled and sequenced using an Illumina NextSeq 2000 (150 bp, paired-end reads) or an NovaSeq X (150 bp, paired-end reads).

value: First true leaves

tag: seed stock

tag: background

tag: developmental stage

value: grown under long day conditions (16h light/ 8 h dark), and transferred to short day conditions (8 h light/ 16 h dark) at 19-DAG


title: Psalmonis Fur knockdown - IPTG induced. Replicate 2

status: Public on Oct 01 2025

type: SRA

city: Santiago

first: Christian

middle: E

last: Hodar

state: Santiago

address: Av. El Libano 5524

department: INTA

country: Chile

institute: Universidad de Chile

description:
Library name: IPTG_Rep2
FUR_IND2

library_source: transcriptomic

data_processing:
The RNA-seq raw data quality was examined using FastQC (S. Andrews, 2010) to detect low quality reads and Illumina adapters, which were subsequently eliminated using BBduk software (Bushnell, 2014). The filtered reads were mapped against the P. salmonis CGR02 genome (GenBank accession N° GCA_001534725.1) using the STAR v2.7.10b RNA-Seq alignment tool. Reads that failed to map to any gene or mapped to multiple genes were removed before expression analysis. Gene quantification was generated using the quantMode option available at STAR program. To identify the differentially expressed genes (DEGs), the gene counts matrices were previously filtered by removing genes with counts in less than two of three replicates by condition. Finally, low expressed genes were discarded using the strategy described in (Chen et al., 2016). RNA-seq data can be accessed at NCBI, BioProject PRJNA1300335. DESeq2 v1.46.0 package (Love et al., 2014) was used to detect DEGs. First, raw count data was used to calculate normalization factors to correct for variations in library depth. Next, gene-specific dispersion values were estimated and refined through shrinkage of gene-wise dispersion. Finally, we fit a negative binomial model to each gene followed by a differential expression test using the Wald significance test. All these calculations were carried out using R software v.4.3.1
Assembly: GCA_001534725.1
Supplementary files format and content: The file counts.furexperiment.csv, contains the counts obtained after the aligning process against the P. salmonis genome. This counts were used in the DE analysis.

molecule: total RNA

organism: Piscirickettsia salmonis

extract_protocol:
P. salmonis strains sgRNA-fur1 and sgRNA-fur2 were grown for 38 hours (mid-exponential phase) at 18°C in NPB supplemented or not with IPTG 100 µM and then were collected by centrifugation 8000 × g for 10 min at 4°C, supernatants were discarded and the pellets were suspended in 750 µL of TRIzol (Thermo Fisher Scientific) and total RNA extraction was carried out according to manufacturer’s instructions. Four micrograms of RNA were treated with Turbo DNA-free Kit (Invitrogen) according to standard protocols. Purified RNA was resuspended in 50 µL of nuclease free water and quantified using a Qubit Fluorometric Quantitation System (Life Technologies). RNA quality was assessed using the 2200 TapeStation Bioanalyzer (Agilent Technologies).
Three libraries for control (uninduced sgRNA-fur1 strain) and three for IPTG-induced sgRNA-fur1 strain were generated at SeqCenter (Pittsburgh, PA), using the TruSeq Stranded Total RNA Library Prep (Illumina), with bacterial rRNA removal. The libraries were paired-end sequenced on a NovaSeq X Plus instrument (Illumina) with read lengths of 150 bp.

tag: cell line

tag: genotype

value: Fur knockdwon

tag: treatment

value: IPTG Induced


title: Normal_1_6_2_4

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: Sample 547

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

molecule: genomic DNA

organism: Homo sapiens

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: age

tag: condition

value: Normal

tag: testis

value: testis


title: WT/pYL27-4NAG 2

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

description:
Library name: Sample 5
raw counts

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Trimmed sequences were mapped
Assembly: NCBI Reference genome (Yarrowia lipolytica CLIB122)
Supplementary files format and content: xlsx format
Supplementary files format and content: raw counts

organism: Yarrowia lipolytica

source_name: yeast strain

growth_protocol: Cells were grown in YNB-GlcNAc to about 0.8 of OD600

extract_protocol:
Total RNA was extracted using Yeast RNA Kit (Omega, China)
RNA libraries were prepared for sequencing using standard Illumina protocols. A total amount of 1 µg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using TruSeq RNA Library Preparation Kit (Illumina, USA) following manufacturer’s recommendations.

treatment_protocol: No treatment

tag: tissue

value: yeast strain

tag: cell type

value: Wild type

value: No


title: Psalmonis Fur knockdown - IPTG induced. Replicate 1

description:
Library name: IPTG_Rep1
FUR_IND1


title: Normal_1_6_2_3

description: Sample 546


title: Col-0, D30, FT, LDSD, EM-seq, chamber B>A

country: USA

description:
Library name: Col-0_D30_FT_LDSD__chamber_B_A
150x 150


title: Col-0, D28, FT, LDSD, EM-seq, chamber B>A

description:
Library name: Col-0_D28_FT_LDSD__chamber_B_A
150x 150


title: Col-0, D26, FT, LDSD, EM-seq, chamber B>A

description:
Library name: Col-0_D26_FT_LDSD__chamber_B_A
150x 150


title: Control, replicate 6, RNA-seq

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description:
Library name: PK6
Zymo-Seq RiboFree Total RNA Library Kit

data_processing:
Read sequences in fastq format were aligned to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: Text document read counts.

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Microprep Kit (Zymo Research, Cat#: R2060) following the manufacturer’s instructions.
Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, Cat#: R3000) was used for library preparation

value: skeletal muscle


title: Normal_1_6_2_2

description: Sample 545


title: Normal_1_6_2_1

description: Sample 544


title: Col-0, D23, FT, LDSD, EM-seq, chamber B>A

description:
Library name: Col-0_D23_FT_LDSD__chamber_B_A
150x 150


title: Control, replicate 8, RNA-seq

description:
Library name: PK8
Zymo-Seq RiboFree Total RNA Library Kit


title: Control, replicate 4, RNA-seq

description:
Library name: PK4
Zymo-Seq RiboFree Total RNA Library Kit


title: Psalmonis control. Replicate 3

description:
Library name: Control_Rep3
FUR_ND3

value: WT

value: Control


title: Control, replicate 7, RNA-seq

description:
Library name: PK7
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_12_8

description: Sample 543


title: Control, replicate 3, RNA-seq

description:
Library name: PK3
Zymo-Seq RiboFree Total RNA Library Kit


title: Psalmonis Fur knockdown - IPTG induced. Replicate 3

description:
Library name: IPTG_rep3
FUR_IND3


title: Col-0, D33, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D33_FT_LD__chamber_B_A
150x 150

value: grown under long day conditions (16h light/ 8 h dark)


title: Psalmonis control. Replicate 1

description:
Library name: Control_Rep1
FUR_ND1


title: Control, replicate 5, RNA-seq

description:
Library name: PK5
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_12_7

description: Sample 542


title: [S. pombe] [p18-p24 input] [wt swi6 (814)] [replicate C]

city: San Francisco

first: Bassem

last: Al-Sady

state: CA

address: 513 Parnassus Ave HSW 1501

institute: UCSF

description: Library name: wtswi6_p18-p24_input_repC

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.39.
first, the custom genome was indexed using the bowtie2-build function of Bowtie2 v2.5.1. Trimmed ChIP-seq reads were aligned to the genome using Bowtie2 v2.5.3.
ChIP-seq reads were then sorted and indexed following SAMtools "view", "sort" and "index" functions.
deepTools v3.5.4  bamCoverage function was used to convert sorted, indexed BAM files to bigWig coverage tracks: -b "$bam_file" -o "$filename_without_extension.bw" --binSize 10 --normalizeUsing CPM --scaleFactor --exactScaling  --effectiveGenomeSize 13000000
Normalized bigWig files were loaded into R v4.3.0 using rtracklayer v1.60.1. Bioconductor Gviz v1.44.2  DataTrack, AnnotationTrack, and GenomeAxisTrack functions were used to visualize ChIP -seq signal tracks from input normalized bigWig files.
Assembly: Genome Assembly ASM294v2 with custom chromosome II. The MAT locus was edited to our custom heterochromatin spreading sensor.
Supplementary files format and content: bigWig

organism: Schizosaccharomyces pombe

source_name: S. pombe

growth_protocol: YES media, 32degreesC, 225RPM shaking until ~OD 2. Then cells were for 2 hours at 18degreesC prior to fixation.

extract_protocol:
600million cells were pelleted and resuspended in room temperature 1XPBS. Cells were fixed in 1.5 mM EGS (final) for 30 minutes at room temperature, followed by 1% formaldehyde (final) for 30 minutes at room temperature. Next glycine was added to a final concentration of 0.25M, incubated 5 minutes at room temperature. Pellets washed twice with cold 1XTBS. Lysate was spun down, pellet was isolated and flash frozen in liquid nitrogen.
Libraries were prepared using NEBNext Mulitplex Oligos for Illumina (E7335L, Lot 10172541; #E6442S, Lot #10236110; and #E6440S Lot #10188082) and Ultra II FS DNA Library Prep Kit for Illumina (E7805L, Lot 10202083) following the manufacturer’s protocol, “Protocol for FS DNA Library Prep Kit (E7805, E6177) with Inputs </=100 ng (NEB)”. 200 pg of input and IP DNA was used as starting material. Libraries were amplified using 11 cycles via PCR. NEBNext sample purification beads (E6178S, Lot 10185312) were used to clean up PCR-enriched adaptor-ligated DNA. DNA concentration was quantified using a Qubit4 Fluorometer and quality was checked by a 4200 TapeStation instrument (Agilent). Libraries were pooled to equimolar quantities for sequencing.

tag: genotypes

tag: chip antibody

value: no antibody input

value: S. pombe


title: Col-0, D26, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D26_FT_LD__chamber_B_A
150x 150


title: Normal_1_6_12_6

description: Sample 541


title: Control, replicate 1, RNA-seq

description:
Library name: PK1
Zymo-Seq RiboFree Total RNA Library Kit


title: [S. pombe] [input Flag ChIP] [wt swi6 (1195)] [replicate C]

description: Library name: wtswi6_FlagSwi6_input_repC

value: flag-wtswi6 (1195)


title: Col-0, D21, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D21_FT_LD__chamber_B_A
150x 150

value: First true leaves


title: Patient-derived cells, VUS, Day 24, biol rep 3

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

description: Library name: Clone-I-day-24-ND4

data_processing:
Raw sequencing reads were processed using the ENCODE/DCC pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Reads were aligned to GRCh38 and quantified using kallisto.
Kallisto quantificiation files were read into edgeR/limma using the tximport package in R to generate counts matrices
Assembly: GRCh38
Supplementary files format and content: RawCountsMatrix_Day18.tsv contains the Kallisto-quantified counts of all genes for iPSC and Day 18 samples
Supplementary files format and content: RawCountsMatrix_Day24.tsv contains the Kallisto-quantified counts of all genes for the Day 24 samples only

source_name: Patient-derived, Day 24

growth_protocol: Patient-derived iPSCs were grown in Matrigel-coated plates in TeSR-E8 media. The STEMdiff SMADi Neural Induction Kit was used to stimulate differentiation of iPSCs into NPCs

extract_protocol:
RNA was extracted from cells using the RNeasy Minikit (Qiagen).
RNA integrity was determined using the Agilent TapeStation system (Genomics WA). RNA sequencing was performed according to SureSelect Strand-Specific RNA Library preparation for Illumina Multiplexed sequencing, paired-end, 100 bp, 30 M read RNA sequencing on the NOVAseq 6000 platform (Illumina, USA) at Genomics WA (Perth, Australia).

value: neural progenitor cell

tag: clone

value: I


title: Control, replicate 10, RNA-seq

description:
Library name: PK10
Zymo-Seq RiboFree Total RNA Library Kit


title: [S. pombe] [p18-p24 Swi6 ChIP] [wt swi6 (814)] [replicate C]

description: Library name: wtswi6_p18-p24 Swi6_repC


title: Normal_1_6_12_4

description: Sample 539


title: Patient-derived cells, VUS, Day 24, biol rep 2

description: Library name: Clone-I-day-24-ND3


title: Col-0, D19, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D19_FT_LD__chamber_B_A
150x 150


title: Normal_1_6_11_7

description: Sample 538


title: Patient-derived cells, VUS, Day 24, biol rep 1

description: Library name: Clone-I-day-24-ND1


title: Col-0, D17, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D17_FT_LD__chamber_B_A
150x 150


title: Psalmonis control. Replicate 2

description:
Library name: Control_Rep2
FUR_ND2


title: Col-0, D15, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D15_FT_LD__chamber_B_A
150x 150


title: Normal_1_6_11_6

description: Sample 537


title: Control, replicate 2, RNA-seq

description:
Library name: PK2
Zymo-Seq RiboFree Total RNA Library Kit


title: [S. pombe] [input Flag ChIP] [wt swi6 (1197)] [replicate B]

description: Library name: wtswi6_FlagSwi6_input_repB

value: flag-wtswi6 (1197)


title: Col-0, D34, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D34_FT_LDSD__chamber_A_B
150x 150

value: grown under long day conditions (16h light/ 8 h dark), and transferred to short day conditions (8 h light/ 16 h dark) at 19-DAG


title: Col-0, D28, FT, LD, EM-seq, chamber B>A

description:
Library name: Col-0_D28_FT_LD__chamber_B_A
150x 150


title: Col-0, D39, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D39_FT_LDSD__chamber_A_B
150x 150


title: Normal_1_6_11_5

description: Sample 536

value: male

value: Normal


title: Patient-derived cells, WT, Day 24, biol rep 2

description: Library name: Clone-D-day-24-ND3

value: D


title: [S. pombe] [p18-p24 Swi6 ChIP] [wt swi6 (814)] [replicate B]

description: Library name: wtswi6_p18-p24 Swi6_repB


title: Patient-derived cells, WT, Day 24, biol rep 1

description: Library name: Clone-D-day-24-ND1


title: Normal_1_6_12_5

description: Sample 540

value: testis


title: Patient-derived cells, VUS, Day 18, biol rep 3

description: Library name: Clone-I-NDiff-4-Day-18

source_name: Patient-derived, Day 18


title: Normal_1_6_11_3

description: Sample 535


title: Col-0, D28, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D28_FT_LDSD__chamber_A_B
150x 150


title: [S. pombe] [Flag-Swi6 ChIP] [wt swi6 (1195)] [replicate C]

description: Library name: wtswi6_FlagSwi6_repC

value: M2 FLAG (Sigma F1804)


title: [S. pombe] [p18-p24 input] [wt swi6 (814)] [replicate B]

description: Library name: wtswi6_p18-p24_input_repB


title: [S. pombe] [p18-p24 input] [wt swi6 (814)] [replicate A]

description: Library name: wtswi6_p18-p24_input_repA


title: Col-0, D25, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D25_FT_LDSD__chamber_A_B
150x 150


title: Patient-derived cells, VUS, Day 0, biol rep 3

description: Library name: Clone-I-NDiff-4-Day-0

source_name: Patient-derived, Day 0

value: induced pluripotent stem cell


title: [S. pombe] [input Flag-ChIP] [wt swi6 (1196)] [replicate A]

description: Library name: wtswi6_FlagSwi6_input_repA

value: flag-wtswi6 (1196)


title: [S. pombe] [p18-p24 Swi6 ChIP] [wt swi6 (814)] [replicate A]

description: Library name: wtswi6_p18-p24 Swi6_repA


title: Patient-derived cells, WT, Day 18, biol rep 3

description: Library name: Clone-D-NDiff-4-Day-18


title: Patient-derived cells, WT, Day 24, biol rep 3

description: Library name: Clone-D-day-24-ND4


title: Normal_1_6_10_8

description: Sample 532


title: Normal_1_6_10_7

description: Sample 531


title: Col-0, D23, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D23_FT_LDSD__chamber_A_B
150x 150


title: [S. pombe] [Flag-Swi6 ChIP] [wt swi6 (1196)] [replicate A]

description: Library name: wtswi6_FlagSwi6_repA


title: Col-0, D39, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D39_FT_LD__chamber_A_B
150x 150


title: Normal_1_6_10_6

description: Sample 530


title: Patient-derived cells, VUS, Day 18, biol rep 2

description: Library name: Clone-I-NDiff-3-Day-18


title: [S. pombe] [input Flag-ChIP] [S6/A swi6 (4652_avail7) (1204)] [replicate C]

description: Library name: S6Aswi6_input_repC


title: Col-0, D34, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D34_FT_LD__chamber_A_B
150x 150


title: Normal_1_6_10_5

description: Sample 529


title: Patient-derived cells, VUS, Day 0, biol rep 2

description: Library name: Clone-I-NDiff-3-Day-0


title: [S. pombe] [Flag-Swi6 ChIP] [wt swi6 (1197)] [replicate B]

description: Library name: wtswi6_FlagSwi6_repB


title: Normal_1_6_11_2

description: Sample 534


title: [S. pombe] [FlagSwi6 ChIP] [S6/A swi6 (4652_avail7) (1204)] [replicate C]

description: Library name: S6Aswi6_FlagSwi6_repC


title: Col-0, D28, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D28_FT_LD__chamber_A_B
150x 150


title: Normal_1_6_11_1

description: Sample 533


title: Normal_1_6_10_4

description: Sample 528


title: Col-0, D30, FT, LDSD, EM-seq, chamber A>B

description:
Library name: Col-0_D30_FT_LDSD__chamber_A_B
150x 150


title: [S. pombe] [input Flag-ChIP] [S6/A swi6 (4652_avail6) (1203)] [replicate B]

description: Library name: S6Aswi6_input_repB


title: Normal_1_6_10_3

description: Sample 527


title: Col-0, D25, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D25_FT_LD__chamber_A_B
150x 150


title: Patient-derived cells, WT, Day 0, biol rep 2

description: Library name: Clone-D-NDiff-3-Day-0


title: Col-0, D20, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D20_FT_LD__chamber_A_B
150x 150


title: Patient-derived cells, WT, Day 18, biol rep 2

description: Library name: Clone-D-NDiff-3-Day-18


title: Patient-derived cells, VUS, Day 18, biol rep 1

description: Library name: Clone-I-NDiff-1-Day-18


title: Patient-derived cells, WT, Day 0, biol rep 3

description: Library name: Clone-D-NDiff-4-Day-0


title: Normal_1_6_10_1

description: Sample 525


title: [S. pombe] [input Flag-ChIP] [S6/A swi6 (4652_avail5) (1202)] [replicate A]

description: Library name: S6Aswi6_input_repA


title: [S. pombe] [FlagSwi6 ChIP] [S6/A swi6 (4652_avail6) (1203)] [replicate B]

description: Library name: S6Aswi6_FlagSwi6_repB


title: Patient-derived cells, VUS, Day 0, biol rep 1

description: Library name: Clone-I-NDiff-1-Day-0


title: Col-0, D15, FT, LD, EM-seq, chamber A>B

description:
Library name: Col-0_D15_FT_LD__chamber_A_B
150x 150


title: [S. pombe] [FlagSwi6 ChIP] [S6/A swi6 (4652_avail5) (1202)] [replicate A]

description: Library name: S6Aswi6_FlagSwi6_repA


title: Normal_1_6_1_8

description: Sample 524


title: [S. pombe] [input Flag-ChIP] [S18/24A swi6 (1199)] [replicate C]

description: Library name: S18AS24Aswi6_input_repC


title: h1.1/1.2, D23, FT, LD, EM-seq

description:
Library name: h1.1/1.2_D23_FT_LD
150x 150


title: h1.1/1.2, D30, FT, LD, EM-seq

description:
Library name: h1.1/1.2_D30_FT_LD
150x 150


title: Normal_1_6_1_7

description: Sample 523


title: [S. pombe] [FlagSwi6 ChIP] [S18/24A swi6 (1199)] [replicate C]

description: Library name: S18AS24Aswi6_FlagSwi6_repC


title: Patient-derived cells, WT, Day 0, biol rep 1

description: Library name: Clone-D-NDiff-1-Day-0


title: h1.1/1.2, D18, FT, LD, EM-seq

description:
Library name: h1.1/1.2_D18_FT_LD
150x 150


title: Patient-derived cells, WT, Day 18, biol rep 1

description: Library name: Clone-D-NDiff-1-Day-18


title: h1.1/1.2, D13, FT, LD, EM-seq

description:
Library name: h1.1/1.2_D13_FT_LD
150x 150


title: NPC43_con

city: 广州

first: 清双

last: 罗

address: 南方医科大学

institute: 第三附属医院

description: Library name: Sample 1

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: The sequenced reads were single-end mapped to reference genome sequences GRCh38
Supplementary files format and content: FPKMs

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: undifferentiated Nasopharyngeal carcinoma cell

value: empty vector pcDNA3.1 were transfected for 48h


title: NPC43_zta

description: Library name: Sample 2

value: pcDNA3.1-BZLF1(+) were transfected for 48h


title: Normal_1_6_1_5

description: Sample 521


title: Normal_1_6_1_6

description: Sample 522


title: Normal_1_6_10_2

description: Sample 526


title: [S. pombe] [input Flag-ChIP] [S18/24A swi6 (1198)] [replicate B]

description: Library name: S18AS24Aswi6_input_repB

value: no antibody input

value: S. pombe


title: [S. pombe] [input Flag-ChIP] [S18/24A swi6 (1200)] [replicate A]

description: Library name: S18AS24Aswi6_input_repA


title: [S. pombe] [FlagSwi6 ChIP] [S18/24A swi6 (1198)] [replicate B]

description: Library name: S18AS24Aswi6_FlagSwi6_repB


title: Normal_1_6_1_3

description: Sample 519


title: Normal_1_6_1_4

description: Sample 520


title: RA6

city: Hangzhou

first: Feiyang

last: Ji

state: None Selected

address: 3 Qingchun East Road

institute: zhejiang university

description: Library name: Sample 18

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

molecule: polyA RNA

source_name: synovial tissue in the joint capsule

extract_protocol:
Total RNA was extracted using the QIAGEN  RNeasy  Lipid Tissue  Mini  Kit according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: synovial tissue in the joint capsule

tag: disease

value: rheumatoid arthritis


title: tcx5/6, D45, FT, LD, EM-seq

description:
Library name: tcx5/6_D45_FT_LD
150x 150

value: First true leaves

value: grown under long day conditions (16h light/ 8 h dark)


title: RA5

description: Library name: Sample 17


title: [S. pombe] [FlagSwi6 ChIP] [S18/24A swi6 (1200)] [replicate A]

description: Library name: S18AS24Aswi6_FlagSwi6_repA


title: tcx5/6, D23, FT, LD, EM-seq

description:
Library name: tcx5/6_D23_FT_LD
150x 150


title: Normal_1_6_1_2

description: Sample 518


title: [S. pombe] [input ChIP] [S18/24A swi6 (859)] [replicate C]

description: Library name: S18AS24Aswi6_p18-p24_input_repC


title: RA4

description: Library name: Sample 16


title: Normal_1_6_1_1

description: Sample 517


title: RA3

description: Library name: Sample 15


title: tcx5/6, D18, FT, LD, EM-seq

description:
Library name: tcx5/6_D18_FT_LD
150x 150


title: Normal_1_5_9_8

description: Sample 516


title: tcx5/6, D13, FT, LD, EM-seq

description:
Library name: tcx5/6_D13_FT_LD
150x 150


title: [S. pombe] [input ChIP] [S18/24A swi6 (858)] [replicate B]

description: Library name: S18AS24Aswi6_p18-p24_input_repB


title: RA2

description: Library name: Sample 14


title: [S. pombe] [p18-p24 Swi6 ChIP] [S18/24A swi6 (859)] [replicate C]

description: Library name: S18AS24Aswi6_p18-p24 Swi6_repC


title: RA1

description: Library name: Sample 13


title: OA6

description: Library name: Sample 12

value: osteoarthritis


title: lin37a/b, D23, FT, LD, EM-seq

description:
Library name: lin37a/b_D23_FT_LD
150x 150


title: tcx5/6, D30, FT, LD, EM-seq

description:
Library name: tcx5/6_D30_FT_LD
150x 150


title: lin37a/b, D30, FT, LD, EM-seq

description:
Library name: lin37a/b_D30_FT_LD
150x 150


title: [S. pombe] [input ChIP] [S18/24A swi6 swi6 (851)] [replicate A]

description: Library name: S18AS24Aswi6_p18-p24_input_repA


title: OA5

description: Library name: Sample 11


title: Normal_1_5_9_6

description: Sample 514

value: male


title: Normal_1_5_9_2

description: Sample 512

value: Normal


title: lin37a/b, D18, FT, LD, EM-seq

description:
Library name: lin37a/b_D18_FT_LD
150x 150


title: ham8-24h-3_1

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

description: Library name: Sample 18

data_processing:
The data from high-throughput sequencing were analyzed using the Omicsmart tools, a free online platform for data analysis (www.omicsmart.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The  WT, ΔAoham4 and ΔAoham8 strains were cultured in a PDA medium for 7 days. Afterward, 200 C. elegans cells were added to each plate for 24 hours.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

value: Fungal hyphae cells

value: Aoham8 knockdown


title: Normal_1_5_9_1

description: Sample 511

value: testis


title: OA4

description: Library name: Sample 10


title: OA3

description: Library name: Sample 9


title: [S. pombe] [p18-p24 Swi6 ChIP] [S18/24A swi6 (851)] [replicate A]

description: Library name: S18AS24Aswi6_p18-p24 Swi6_repA


title: ham8-24h-2_1

description: Library name: Sample 17


title: aly1/3, D23, FT, LD, EM-seq

description:
Library name: aly1/3_D23_FT_LD
150x 150


title: Normal_1_5_8_6

description: Sample 510


title: ham8-24h-1_1

description: Library name: Sample 16


title: Normal_1_5_9_7

description: Sample 515


title: lin37a/b, D13, FT, LD, EM-seq

description:
Library name: lin37a/b_D13_FT_LD
150x 150


title: [S. pombe] [p18-p24 Swi6 ChIP] [S18/24A swi6 (858)] [replicateB]

description: Library name: S18AS24Aswi6_p18-p24 Swi6_repB


title: Normal_1_5_8_4

description: Sample 509


title: aly1/3, D18, FT, LD, EM-seq

description:
Library name: aly1/3_D18_FT_LD
150x 150


title: OA1

description: Library name: Sample 7


title: OA2

description: Library name: Sample 8


title: ham8-0h-3_1

description: Library name: Sample 15


title: aly1/3, D13, FT, LD, EM-seq

description:
Library name: aly1/3_D13_FT_LD
150x 150


title: Normal_1_5_8_3

description: Sample 508


title: NC6

description: Library name: Sample 6

value: trauma


title: Normal_1_5_9_4

description: Sample 513


title: aly1/2, D30, FT, LD, EM-seq

description:
Library name: aly1/2_D30_FT_LD
150x 150


title: NC5

description: Library name: Sample 5


title: aly1/3, D30, FT, LD, EM-seq

description:
Library name: aly1/3_D30_FT_LD
150x 150


title: Normal_1_5_8_2

description: Sample 507


title: ham8-0h-2_1

description: Library name: Sample 14


title: aly1/2, D23, FT, LD, EM-seq

description:
Library name: aly1/2_D23_FT_LD
150x 150


title: ham4-24h-3_1

description: Library name: Sample 12

value: Aoham4 knockdown


title: NC4

description: Library name: Sample 4


title: aly1/2, D18, FT, LD, EM-seq

description:
Library name: aly1/2_D18_FT_LD
150x 150


title: NC3

description: Library name: Sample 3


title: ham4-24h-2_1

description: Library name: Sample 11


title: Normal_1_5_7_8

description: Sample 506


title: Normal_1_5_7_6

description: Sample 505


title: NC2

description: Library name: Sample 2


title: ham4_24h_1_1

description: Library name: Sample 10


title: NC1

description: Library name: Sample 1


title: Col-0, D45, young, rosette, LD, EM-seq

description:
Library name: Col-0_D45_young_rosette_LD
150x 150

source_name: young rosette leaves

value: young rosette leaves


title: Ws-2, embryo, LD, EM-seq

description:
Library name: Ws-2_embryo_LD
150x 150

source_name: green embryo

value: green embryo

value: silique


title: Normal_1_5_7_4

description: Sample 503


title: Normal_1_5_7_2

description: Sample 502


title: Muscle, Juvenile Dermatomyositis

city: Jinan

first: FUCHEN

last: Liu

state: 山东省

address: No 107, West Wenhua Road, Lixia District

institute: Qilu Hospital

description: Library name: S2

data_processing:
Sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings.
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi - res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low - res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Frozen Muscle section

extract_protocol:
RNA was extracted from tissue sections using the RNeasy Plus Micro Kit (Qiagen). The tissue was scraped from slides and homogenized in lysis buffer, followed by RNA extraction according to the manufacturer’s protocol. RNA quality was assessed using a Bioanalyzer (RIN>=7) and RNA concentration was measured using a Qubit RNA assay. If RNA input was low, RNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
Tissue sections (10 μm thick) were prepared on poly-L-lysine-coated slides and stored at -80°C. After thawing, tissues were permeabilized to allow efficient RNA capture. The mRNA was hybridized with spatially barcoded probes, followed by reverse transcription to generate cDNA. The cDNA was then amplified, fragmented, and ligated with adapters for sequencing. The library quality was assessed using a Bioanalyzer, and sequencing was performed on the Illumina NovaSeq 6000 platform with paired-end reads.

value: Frozen Muscle section

value: Juvenile Dermatomyositis


title: spl2/9/10/11/13/15, embryo, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_embryo_LD
150x 150


title: Normal_1_5_7_1

description: Sample 501


title: ham4_0h_2_1

description: Library name: Sample 8


title: ham8-0h-1_1

description: Library name: Sample 13


title: Muscle, Adult Dermatomyositis

description: Library name: S1

value: Adult Dermatomyositis


title: EB, 7th day, ATAC

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 500 S State St

department: DCMB

institute: University of Michigan

description:
Library name: 8964-KL-1_ATAC
8964-KL-1_barcodes.tsv.gz
8964-KL-1_features.tsv.gz
8964-KL-1_matrix.mtx.gz
8964-KL-1_feature_linkage.bedpe

library_source: genomic single cell

data_processing:
Raw sequencing data were mapped and preprocessed to gene expressions and peaks using CellRanger ARC 2.0.0.
Secondary analyses by CellRanger ARC produced feature linkages between peaks and genes.
Unspliced and spliced mRNA expressions were quantified using STARsolo with the references (GRCh38) provided in CellRanger ARC.
Assembly: GRCh38
Supplementary files format and content: Combined RNA and ATAC count data from CellRanger in zipped Matrix Market format
Supplementary files format and content: STARsolo quantified RNA, unspliced, and spliced matrices in zipped Matrix Market format (Note the barcodes and features tsv files are shared across matrices.)
Supplementary files format and content: CellRanger linkage file in text format
Supplementary files format and content: CellRanger ATAC peak annotation file in text format

source_name: Embryoid body

growth_protocol: ***HSPC and macrophage*** Cell cultures were maintained at 37°C in a 5% CO2 humidified atmosphere. CD34+ hematopoietic stem cells were acquired from the Fred Hutch Hematology core. Frozen CD34+ cells were thawed in serum-free RPMI plus 10mM HEPES, then cultured at 1 x 10^6 cells/ml of STIF medium [Stemspan II medium supplemented with 100 ng/ml stem cell factor, 100 ng/ml thrombopoietin, 100 ng/ml Flt3 ligand (all from Stemcell Technologies), and 100 ng/ml insulin-like growth factor binding protein 2 (R&D Systems)]. Cells were expanded at two and four days post-thaw. Seven days post-thaw, cells were processed for single-cell submission or transferred from STIF into macrophage-stimulating medium (MSM) [SFEM supplemented with 1x Myeloid Expansion Supplement II (Cat# 02694, StemSpanTechnologies) and 20µg/mL IL-6 (R&D Technologies)] for in vitro differentiated macrophages. Differentiating cells were cultured for an additional 7 days in MSM. HSCs were expanded in MSM on day 7 by seeding cells at 250k/well in 24-well plates in 500ul MSM. On day 10, cells were divided four times and maintained in 500µl MSM. On day 14, cells were collected for single-cell analysis. ***EB*** Human induced pluripotent stem cells (iPSCs) were cultured in mTeSR1 medium (STEMCELL, Cat. No. 85850) on Growth Factor Reduced, Matrigel Basement Membrane Matrix (Corning; Cat. No. 354230) coated dishes. mTeSR1 was replaced every day. When cells reached 70-80% confluency, they were passaged by aspirating media, washing with DPBS (Gibco; Cat. No. 14190144), and incubating with StemPro Accutase (Gibco; Cat. No. A1110501) at 37C for 5 minutes. Cells were mixed with DPBS and centrifuged at 300g for 3 minutes. The supernatant was aspirated, resuspended in mTeSR1 medium supplemented with 10 nM y-27632 dihydrochloride ROCK inhibitor (STEMCELL; Cat. No. NC1678100), and counted with a Countess 3 Automated Cell Counter (ThermoFisher Scientific). EBs were formed using the STEMCELL Aggrewell400 protocol (DX21732). Briefly, the AggreWell400 24-well plate was coated with AggreWell Rinsing Solution (STEMCELL; Cat. No. 07010). The dissociated iPSCs were seeded in AggreeWell EB Formation Medium (STEMCELL; Cat. No. 05893) into the AggreWell400 plate at 1,000 cells per microwell, totaling 1.2 x 106 per well. After 24 hours, half the media change was performed. After 48 hours, EBs were harvested using a 40-um Strainer (ThermoFisher Scientific; Cat. No. 22-363-547) and transferred to an ultra-low attachment six-well plate in Essential E6 media (Gibco; Cat. No. A1516401). Media was replaced every other day and flash-frozen on day 7 in E6 media.

extract_protocol:
***HSPC and macrophage*** Cells were washed in 1 x PBS-/- supplemented with 0.04% BSA and sorted using the BigFoot cell sorter (Thermo Fisher) on days 7 or 14. For in vitro-differentiated adherent cells, cells were lifted using enzyme-free cell dissociation buffer (ThermoFisher) before washing and sorting. Nuclei were isolated following the ‘Low Cell Input Nuclei Isolation’ sub-protocol and immediately processed using the Chromium Next GEM Single Cell Multiome + Gene Expression kit. ***EB*** Flash-frozen D7 EBs were thawed on ice. Nuclei isolation was performed according to the 10X Genomics demonstrated protocol ‘Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing’ (CG000375 Rev B). Briefly, EBs were homogenized using a 1000 ul wide-bore tip in lysis buffer and incubated on ice for 5 minutes. Cells were then filtered through a 70 um strainer and centrifuged at 500g for 5 min at 4C. The supernatant was removed and 1 ml of PBS + 1% BSA + 1U/ul RNase inhibitor (Roche; Cat. No. 3335402001) was added and incubated on ice for 5 minutes. The pellet was resuspended using a wide bore tip and centrifuged at 500g for 5 minutes at 4C. The pellet was then resuspended in 100 ul 0.1X lysis buffer and incubated on ice for 2 minutes. 1 ml of buffer was added to mix the pellet and centrifuged at 500 g for 5 minutes at 4C. The supernatant was removed and resuspended in chilled diluted nuclei buffer (10X Genomics). The nuclei were diluted to 3000-8000 nuclei/ul by using a Countess 3 Automated Cell Counter and proceeded to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.
***HSPC and macrophage*** Single Cell Multiome ATAC and Gene Expression libraries were prepared according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide for standard Illumina paired-end sequencing. ***EB*** Single nuclei libraries were generated using the 10X Genomics Chromium Controller following the manufacturer’s protocol for Multiome (ATAC+GEX) analysis. In brief, transposase was added to the nuclei suspension and incubated, before adding barcode and RT master mix and loading into the Chromium Controller chip with appropriate gel beads. Following the generation of single-cell gell bead-in-emulsions (GEMs), reverse transcription of the RNA and barcoding of the fragmented DNA was performed. The resulting product was cleaned and both the cDNA and barcoded, fragmented DNA were amplified. One fraction of this product made the ATAC library via indexing PCR. The other fraction was amplified again to isolate the cDNA further, which was then quantified by Qubit (Invitrogen) and assessed for size on the TapeStation 4200 (Agilent). It underwent enzymatic fragmentation, size selection, adapter ligation, and indexing PCR. Final library quality was assessed using the LabChip GX Touch HT(Revvity) and was quantified by Qubit. Pooled libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). BclConvert software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generated count matrices.
OTHER: Multiome (RNA and ATAC)

value: Embryoid body

value: iPSC


title: ham4_0h_1_1

description: Library name: Sample 7


title: Col-0, D45, cauline, LD, EM-seq

description:
Library name: Col-0_D45_cauline_LD
150x 150

source_name: First cauline leaves

value: First cauline leaves

value: grown under long day conditions (16h light/ 8 h dark)


title: Normal_1_5_6_5

description: Sample 500

value: male

value: Normal


title: WT_24h_3_1

description: Library name: Sample 6

value: Fungal hyphae

value: Fungal hyphae cells

value: WT


title: aly1/2, D13, FT, LD, EM-seq

description:
Library name: aly1/2_D13_FT_LD
150x 150

value: First true leaves


title: Normal_1_5_6_3

description: Sample 498

value: testis


title: Normal_1_5_6_4

description: Sample 499


title: EB, 7th day, RNA

description:
Library name: 8964-KL-1_RNA
8964-KL-1_barcodes.tsv.gz
8964-KL-1_features.tsv.gz
8964-KL-1_matrix.mtx.gz
8964-KL-1_feature_linkage.bedpe

library_source: transcriptomic single cell

molecule: nuclear RNA


title: Normal_1_5_7_5

description: Sample 504


title: Col-0, D30, cauline, LD, EM-seq

description:
Library name: Col-0_D30_cauline_LD
150x 150


title: Col-0, D18, cauline, LD, EM-seq

description:
Library name: Col-0_D18_cauline_LD
150x 150


title: WT_24h_2_1

description: Library name: Sample 5


title: ham4_0h_3_1

description: Library name: Sample 9

value: Aoham4 knockdown


title: Macrophage, 14th day, ATAC

description:
Library name: 9060-MV-3_ATAC
9060-MV-3_barcodes.tsv.gz
9060-MV-3_features.tsv.gz
9060-MV-3_matrix.mtx.gz
9060-MV-3_feature_linkage.bedpe

source_name: Blood

value: Blood

value: Primary Cells

value: Differentiated Macrophages


title: WT_24h_1_1

description: Library name: Sample 4


title: Macrophage, 14th day, RNA

description:
Library name: 9060-MV-3_RNA
9060-MV-3_barcodes.tsv.gz
9060-MV-3_features.tsv.gz
9060-MV-3_matrix.mtx.gz
9060-MV-3_feature_linkage.bedpe


title: Col-0, D8, cauline, LD, EM-seq

description:
Library name: Col-0_D8_cauline_LD
150x 150


title: WT_0h_3_1

description: Library name: Sample 3


title: Normal_1_5_5_8

description: Sample 496


title: HSPC, 7th day, ATAC

description:
Library name: 8489-MV-1_ATAC
8489-MV-1_barcodes.tsv.gz
8489-MV-1_features.tsv.gz
8489-MV-1_matrix.mtx.gz
8489-MV-1_feature_linkage.bedpe

value: Mobilized CD34+ Hematopoietic Stem and Progenitor Cells


title: Ws-2, D45, FT, LD, EM-seq

description:
Library name: Ws-2_D45_FT_LD
150x 150


title: Normal_1_5_5_7

description: Sample 495


title: Ws-2, D30, FT, LD, EM-seq

description:
Library name: Ws-2_D30_FT_LD
150x 150


title: Ws-2, D23, FT, LD, EM-seq

description:
Library name: Ws-2_D23_FT_LD
150x 150


title: Normal_1_5_5_6

description: Sample 494


title: HCT116_si11_rep3

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

data_processing:
The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”. The resulting filtered reads were aligned to their respective reference genome using STAR aligner (v2.7.10b) with default parameters. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Exon mapped reads were counted using featureCounts from the subread package (v2.0.6). ATAC-seq datasets were processed to remove the Nextera adapter (CTGTCTCTTATACACATCT) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”115. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2122). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1). Reads were further processed using alignmentSieve from deepTools (v3.5.5) to account for transposon dimerization before insertion. Positive and negative strand alignments were shifted by +4 bp and −5 bp, respectively. Additionally, fragments of 100 bp, corresponding to nucleosome-free regions (NFRs), were retained with the parameters “--minMappingQuality 25 --maxFragmentLength 100 --ATACshift --BED”. Peaks were called on the resulting BEDPE files using MACS3 (v3.0.1) MACS3 with the parameters “--call-summits --bdg --nomodel --nolambda --gsize hs --keep-dup all --format BEDPE --qvalue 0.05”. The predicted peaks were filtered for ENCODE project blacklisted regions using BEDTools (v2.31.0) intersect.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: HCT116_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: HCT116_si11_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_si11_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_si11_rna_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: mESC_diff_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_nfr_atac_raw_counts.tsv  is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: mESC_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
To prepare samples for RNA-seq, 3 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
The ATAC-seq library was prepared as described in Corces, M.R. et al.Nat Methods, 2017. After quality control using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), the libraries were sequenced (150 bp paired-end reads) on an Illumina HiSeq Sequencer (Illumina Inc., San Diego, CA). For RNA-seq, the quality of the isolated RNA was determined using a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further used for library preparation. The Illumina Ribo Zero Plus (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (25-1000 ng) were depleted of ribosomal RNA and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before ligation of an anchor. Fragments containing the anchor on both ends were selectively enriched with PCR at the same time adding the index with unique dual indexes (UDI). The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The libraries were normalized to 10 nM in Tris-HCl 10 mM, pH8.5 with 0.1% Tween20.

value: Human colon cancer cell line


title: HSPC, 7th day, RNA

description:
Library name: 8489-MV-1_RNA
8489-MV-1_barcodes.tsv.gz
8489-MV-1_features.tsv.gz
8489-MV-1_matrix.mtx.gz
8489-MV-1_feature_linkage.bedpe


title: Ws-2, D18, FT, LD, EM-seq

description:
Library name: Ws-2_D18_FT_LD
150x 150


title: MK801 device, pooled fraction, rep 3

first: Sanjay

last: Kumar

address: 205 Stanley Hall, University of California

department: Bioengineering

description:
Library name: Sample09
column name in gene_count.xls: B4

data_processing:
Data processing was performed by Novogene. Data filtering was performed to remove low-quality reads or reads with adapters.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Mapped regions were classified as exons, introns, or intergenic regions.
Gene expression quantification was performed using featureCounts v1.5.0-p3, which was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38
Supplementary files format and content: .xls file with FPKM for each sample

source_name: cell line

growth_protocol: GBM43 cells were cultured in DMEM (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin, and 1% (v/v) Glutamax

extract_protocol:
For control devices, invasive cells were physically separated from the non-invasive “core” cells using a scalpel. For MK-801 treated devices, the invasive fractions were not large enough to isolate separately from the core, so both fractions were pooled for these samples.  Cells were isolated by degrading the hydrogel with hyaluronidase and centrifuging to get a cell pellet. RNA was then extracted using Trizol (Invitrogen) according to manufacturer's instructions.
Isolated RNA was sent to Novogene for library construction, quality control, and sequencing. In brief, mRNA was purified from total RNA using poly-T oligo–attached magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers followed by the second-strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with a Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: MK801 devices were treated with 50 uM MK801. Control devices received equivalent volume of vehicle (DMSO).

value: cell line

value: glioblastoma


title: Normal_1_5_5_4

description: Sample 493


title: HCT116_si11_rep2


title: MK801 device, pooled fraction, rep 2

description:
Library name: Sample08
column name in gene_count.xls: B2


title: MK801 device, pooled fraction, rep 1

description:
Library name: Sample07
column name in gene_count.xls: B1


title: HCT116_ctrl_rep3


title: Normal_1_5_6_2

description: Sample 497


title: Normal_1_5_5_3

description: Sample 492


title: Normal_1_5_5_1

description: Sample 491


title: HCT116_ctrl_rep2


title: Control device, invasive fraction, rep 2

description:
Library name: Sample05
column name in gene_count.xls: A2i

value: control


title: Normal_1_5_4_8

description: Sample 490


title: Control device, invasive fraction, rep 3

description:
Library name: Sample06
column name in gene_count.xls: A4i


title: HCT116_si11_rep1


title: Ws-2, D13, FT, LD, EM-seq

description:
Library name: Ws-2_D13_FT_LD
150x 150

source_name: First true leaves

value: grown under long day conditions (16h light/ 8 h dark)


title: Control device, invasive fraction, rep 1

description:
Library name: Sample04
column name in gene_count.xls: A1i


title: Ws-0, D23, FT, LD, EM-seq

description:
Library name: Ws-0_D23_FT_LD
150x 150


title: Normal_1_5_4_7

description: Sample 489

source_name: testis

value: male


title: WT_0h_1_1

description: Library name: Sample 1


title: WT_0h_2_1

description: Library name: Sample 2


title: HCT116_ctrl_rep1


title: Normal_1_5_4_6

description: Sample 488

value: Normal


title: Ws-0, D18, FT, LD, EM-seq

description:
Library name: Ws-0_D18_FT_LD
150x 150


title: Sample 8 P-BCMA-ALLO1 ADT

city: San Diego

first: Hubert

last: Tseng

address: 9390 Towne Centre Drive Suite 200

institute: Poseida Therapeutics

description: processed data including gene expression and antibody capture features together; compressed .tar.gz file with barcodes.tsv.gz, features.tsv.gz, matrix.mtx together, demultiplexed to each sample

data_processing:
CellRanger 7.0.1 was used to get barcodes and counts
Assembly: GRCh38
Supplementary files format and content: CellRanger output: features.tsv, barcodes.tsv, and matrix.mtx
Supplementary files format and content: features_reference.csv
Library strategy: CITE-Seq

source_name: CAR-T cells

extract_protocol:
P-BCMA-ALLO1 lots were thawed and rested overnight in cell culture media (RPMI-1640 + 10% FBS). After rest, the cells were FACS sorted for viable cells by Live/Dead staining (ThermoFisher). Viable cells were recovered and stained by CITESeq for both protein and hashing. 3 lots were combined into 1 sample before running the cells on the 10X Chromium using the Single Cell 3' v3 kit.
Libraries were constructed following the manufacturer's instructions for the 10X Single Cell 3' v3 kit
CITESeq libraries for both protein and hashtag individually in addition to libraries for gene expression

value: CAR-T cells


title: Control device, core fraction, rep 3

description:
Library name: Sample03
column name in gene_count.xls: A4c


title: Normal_1_5_4_5

description: Sample 487


title: Sample 8 P-BCMA-ALLO1 HTO


title: Ws-0, D13, FT, LD, EM-seq

description:
Library name: Ws-0_D13_FT_LD
150x 150


title: Control device, core fraction, rep 2

description:
Library name: Sample02
column name in gene_count.xls: A2c


title: Normal_1_5_4_2

description: Sample 486


title: Ws-0, D45, FT, LD, EM-seq

description:
Library name: Ws-0_D45_FT_LD
150x 150


title: V9A:rSPL15, D45, FT, LD, EM-seq

description:
Library name: V9A:rSPL15_D45_FT_LD
150x 150


title: Normal_1_5_3_8

description: Sample 485


title: Control device, core fraction, rep 1

description:
Library name: Sample01
column name in gene_count.xls: A1c


title: Sample 8 P-BCMA-ALLO1 GEX


title: Ws-0, D30, FT, LD, EM-seq

description:
Library name: Ws-0_D30_FT_LD
150x 150


title: V9A:rSPL15, D30, FT, LD, EM-seq

description:
Library name: V9A:rSPL15_D30_FT_LD
150x 150


title: Sample 7 P-BCMA-ALLO1 ADT


title: V9A:rSPL15, D23, FT, LD, EM-seq

description:
Library name: V9A:rSPL15_D23_FT_LD
150x 150


title: Normal_1_5_3_6

description: Sample 484


title: Sample 7 P-BCMA-ALLO1 GEX


title: Sample 7 P-BCMA-ALLO1 HTO


title: Sh-2

city: Shangha

first: Zhi-xin

address: No. 507 Zhengmin Road, Yangpu District

institute: Tongji University, School of Medicine

description: Library name: Sh-2

data_processing:
CLC Genomics Workbench y 11.0.1
Assembly: Human genome GRCh38 was used as the reference genome.
Supplementary files format and content: raw counts, FPKM for each Sample

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.

value: lung

value: lung squamous cell carcinoma cell line


title: V9A:rSPL15, D18, FT, LD, EM-seq

description:
Library name: V9A:rSPL15_D18_FT_LD
150x 150

value: First true leaves


title: Normal_1_5_3_5

description: Sample 483

value: testis


title: Normal_1_5_3_4

description: Sample 482


title: Sample 6 P-BCMA-ALLO1 ADT


title: Sh-1

description: Library name: Sh-1


title: Con-3

description: Library name: Con-3

value: Sh-NC


title: spl2/9/10/11/13/15, D45, FT, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_D45_FT_LD
150x 150


title: Sample 6 P-BCMA-ALLO1 HTO


title: Normal_1_5_3_3

description: Sample 481


title: Con-2

description: Library name: Con-2


title: spl2/9/10/11/13/15, D30, FT, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_D30_FT_LD
150x 150


title: Con-1

description: Library name: Con-1


title: Normal_1_5_3_1

description: Sample 480


title: Normal_1_5_2_7

description: Sample 479


title: spl2/9/10/11/13/15, D23, FT, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_D23_FT_LD
150x 150


title: Sh-3

description: Library name: Sh-3


title: Sample 5 P-BCMA-ALLO1 ADT


title: Normal_1_5_2_6

description: Sample 478


title: Sample 6 P-BCMA-ALLO1 GEX


title: Sample 5 P-BCMA-ALLO1 HTO


title: S75_HEK293-AQP4-EmGFP biol rep 3

city: Innsbruck

first: Markus

last: Reindl

address: Innrain 66/2

department: Clinical Department of Neurology

country: Austria

institute: Maedical University of Innsbruck

description:
Library name: S75
Column name in gene_count_preprocessed_mev_data_reindl.gct: S75

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software by Novogene. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. Hisat2 was used by Novogene as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The program featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: The .gct file contains the raw gene counts for each sample (one matrix table for all samples). All genes with <20 counts in all samples were removed.
Supplementary files format and content: all gene counts

growth_protocol: Human primary astrocytes (HA), isolated from human cerebral cortex, were purchased by ScienCell (Lot. No. 33619, Sciencell Research Laboratories, San Diego, CA). For experiments, solely passages 3 to 5 were used. HA were cultured in 2 µg/cm2 poly-L-lysine coated flasks (Sciencell Research Laboratories, San Diego, CA) in astrocyte medium AM (Innoprot, Derio, Spain), containing 2% FCS, 1% P/S and 1% astrocyte growth supplement. Medium was exchanged every other day and cells were passaged when 90% dense. The glioblastoma cell line U-87 MG (ATCC; LGC Standards GmbH, Wesel, Germany) was genetically modified for a stable protein overexpression. Thereby, an overexpression of enhanced cyan fluorescent protein (ECFP) with (U-87MG-AQP4-ECFP) or without (U-87MG-ECFP) AQP4M23 in U-87 MG cells was obtained via lentiviral infection. The vectors were pLIB-MCS-ECFP-iresNeo and pLIB-MCS-AQP4m23-ECFP-iresNeo.  Cells were selected using 10 µg/mL neomycine for 72 hours. HEK293A and U-87 MG cell lines were cultured in DMEM high glucose, 10% FCS and 1% non-essential amino acids and passaged twice a week.

extract_protocol:
Isolation of total RNA was done according to the protocol of the RNeasy Mini Kit (QIAGEN, Hilden, Germany). After quantity and quality determination by a NanoDrop™ System (Thermo Fisher Scientific, Waltham, MA, USA), total RNA samples were sent for sequencing by the Illumina PE150 technology to Novogene (Martinsried, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: U-87MG-ECFP, U-87MG-AQP4-ECFP, HEK293-AQP4 -EmGFP cells or HA were grown in a 12- or 96-well plate until confluent. Then, they were treated with 40% active or heat-inactivated (45 min. at 56 °C) human complement (Cedarline) in X-VIVO 15 medium (Lonza, Basel, Switzerland) and with or without the mouse monoclonal antibody E5415A (in-house production from E5415A-1H6-68 hybridoma cells, #RCB4883, Riken, Tsukubashi, Ibaraki, Japan) (10 µg/mL), followed by an incubation for 90 min. at 37 °C. Afterwards, the cell supernatant was taken to assess cytotoxicity and cells were harvested for RNA isolation, or immunofluorescence staining of the TCC was performed.

value: human embryonic kidney cells


title: S74_HEK293-AQP4-EmGFP biol rep 2

description:
Library name: S74
Column name in gene_count_preprocessed_mev_data_reindl.gct: S74


title: Sample 5 P-BCMA-ALLO1 GEX


title: V9A:rSPL15, D13, FT, LD, EM-seq

first: Dawei

address: 2151 Berkeley Way

description:
Library name: V9A:rSPL15_D13_FT_LD
150x 150

data_processing:
Reads were preprocessed with TrimGalore 0.6.6 (Babraham Bioinformatics) to remove adaptors
Bismark 0.22.3 (2) was used to map filtered reads to the A. thaliana TAIR10 genome, allowing for 0 mismatch per read in the seed region and removing PCR duplicates.
Methylation values for each cytosine were calculated as #C/(#C+#T) using the Bismark methylation extractor function.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited bed files includes methylation level at single base resolution in CHH, CHG, and CG context for each sample.
Library strategy: EM-seq

extract_protocol:
DNA was isolated using the CTAB method.
EM-seq libraries were constructed following the NEBNext® Enzymatic Methyl-seq Kit protocol with 50 ng initial DNA (25 ng for all embryo samples). Library quality was verified with a KAPA Library Quant Kit and fragment analyzer. Libraries were pooled and sequenced using an Illumina NextSeq 2000 (150 bp, paired-end reads) or an NovaSeq X (150 bp, paired-end reads).


title: S73_HEK293-AQP4-EmGFP biol rep 1

description:
Library name: S73
Column name in gene_count_preprocessed_mev_data_reindl.gct: S73


title: Normal_1_5_2_3

description: Sample 476


title: Sample 4 P-BCMA-ALLO1 ADT


title: spl2/9/10/11/13/15, D13, FT, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_D13_FT_LD
150x 150


title: spl2/9/10/11/13/15, D18, FT, LD, EM-seq

description:
Library name: spl2/9/10/11/13/15_D18_FT_LD
150x 150


title: mir156a/c, mir157a/c, D30, FT, LD, EM-seq

description:
Library name: mir156a/c_mir157a/c_D30_FT_LD
150x 150

value: mir156a/c mir157a/c


title: Sample 4 P-BCMA-ALLO1 HTO

description: processed data including gene expression and antibody capture features together; compressed .tar.gz file with barcodes.tsv.gz, features.tsv.gz, matrix.mtx together, demultiplexed to each sample


title: Normal_1_5_2_2

description: Sample 475


title: Normal_1_5_2_4

description: Sample 477


title: S71_HEK293-AQP4-EmGFP IC biol rep 2

description:
Library name: S71
Column name in gene_count_preprocessed_mev_data_reindl.gct: S71

value: inactive human complement


title: Sample 4 P-BCMA-ALLO1 GEX


title: Normal_1_5_12_8

description: Sample 474


title: mir156a/c, mir157a/c, D23, FT, LD, EM-seq

description:
Library name: mir156a/c_mir157a/c_D23_FT_LD
150x 150


title: S70_HEK293-AQP4-EmGFP IC biol rep 1

description:
Library name: S70
Column name in gene_count_preprocessed_mev_data_reindl.gct: S70


title: mir156a/c, mir157a/c, D18, FT, LD, EM-seq

description:
Library name: mir156a/c_mir157a/c_D18_FT_LD
150x 150


title: mir156a/c, mir157a/c, D13, FT, LD, EM-seq

description:
Library name: mir156a/c_mir157a/c_D13_FT_LD
150x 150


title: S68_HEK293-AQP4-EmGFP AC biol rep 2

description:
Library name: S68
Column name in gene_count_preprocessed_mev_data_reindl.gct: S68

value: active human complement


title: Sample 3 P-BCMA-ALLO1 ADT


title: Normal_1_5_12_6

description: Sample 472


title: S69_HEK293-AQP4-EmGFP AC biol rep 3

description:
Library name: S69
Column name in gene_count_preprocessed_mev_data_reindl.gct: S69


title: S67_HEK293-AQP4-EmGFP AC biol rep 1

description:
Library name: S67
Column name in gene_count_preprocessed_mev_data_reindl.gct: S67


title: Normal_1_5_12_4

description: Sample 471


title: S72_HEK293-AQP4-EmGFP IC biol rep 3

description:
Library name: S72
Column name in gene_count_preprocessed_mev_data_reindl.gct: S72


title: Normal_1_5_12_7

description: Sample 473


title: Sample 3 P-BCMA-ALLO1 HTO


title: S66_HEK293-AQP4-EmGFP E5415A+IC biol rep 3

description:
Library name: S66
Column name in gene_count_preprocessed_mev_data_reindl.gct: S66

value: anti-AQP4 antibody E5415A + inactive human complement


title: mir156a/b/c/d, D45, FT, LD, EM-seq

description:
Library name: mir156a/b/c/d_D45_FT_LD
150x 150


title: Normal_1_5_12_2

description: Sample 470


title: mir156a/b/c/d, D30, FT, LD, EM-seq

description:
Library name: mir156a/b/c/d_D30_FT_LD
150x 150


title: mir156a/c, mir157a/c, D45, FT, LD, EM-seq

description:
Library name: mir156a/c_mir157a/c_D45_FT_LD
150x 150


title: Sample 2 P-BCMA-ALLO1 HTO


title: Sample 3 P-BCMA-ALLO1 GEX


title: mir156a/b/c/d, D18, FT, LD, EM-seq

description:
Library name: mir156a/b/c/d_D18_FT_LD
150x 150


title: S65_HEK293-AQP4-EmGFP E5415A+IC biol rep 2

description:
Library name: S65
Column name in gene_count_preprocessed_mev_data_reindl.gct: S65


title: Sample 2 P-BCMA-ALLO1 ADT


title: Normal_1_5_11_7

description: Sample 468


title: Sample 2 P-BCMA-ALLO1 GEX


title: mir156a/b/c/d, D23, FT, LD, EM-seq

description:
Library name: mir156a/b/c/d_D23_FT_LD
150x 150


title: S64_HEK293-AQP4-EmGFP E5415A+IC biol rep 1

description:
Library name: S64
Column name in gene_count_preprocessed_mev_data_reindl.gct: S64


title: Normal_1_5_11_6

description: Sample 467


title: S62_HEK293-AQP4-EmGFP E5415A+AC biol rep 2

description:
Library name: S62
Column name in gene_count_preprocessed_mev_data_reindl.gct: S62

value: anti-AQP4 antibody E5415A + active human complement


title: Col-0, D9, FT, LD, EM-seq

description:
Library name: Col-0_D9_FT_LD
150x 150


title: Sample 1 P-BCMA-ALLO1 ADT

description: processed data including gene expression and antibody capture features together; compressed .tar.gz file with barcodes.tsv.gz, features.tsv.gz, matrix.mtx together, demultiplexed to each sample


title: Normal_1_5_11_4

description: Sample 465


title: S63_HEK293-AQP4-EmGFP E5415A+AC biol rep 3

description:
Library name: S63
Column name in gene_count_preprocessed_mev_data_reindl.gct: S63


title: Sample 1 P-BCMA-ALLO1 GEX


title: Normal_1_5_11_5

description: Sample 466


title: Sample 1 P-BCMA-ALLO1 HTO


title: Col-0, D30, FT, LD, EM-seq

description:
Library name: Col-0_D30_FT_LD
150x 150


title: Normal_1_5_11_2

description: Sample 463


title: A549 cells,shYTHDF3_3,6h

city: xi'an

first: yajing

last: zhao

address: No. 169, Changle West Road, Xincheng District

institute: Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: A549 cell

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: A549 cell


title: BIHi005-A_Not_Classifiable_5

type: genomic

city: Berlin

first: Eilis

last: Perez

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

hyb_protocol: standard Illumina Protocols

scan_protocol: standard Illumina Protocols

data_processing: Raw DNA methylation data were pre-processed using R (v 4.3.3). Signal intensities were obtained from IDAT files using the Bioconductor package minfi (v 1.40.0) (Aryee et al., 2014). Dye bias correction was performed using the Noob (normal-exponential out-of-band) method with the preprocessNoob function without “between-array normalisation” (Triche et al., 2013). Data filtering steps included the removal of probes with detection p-values greater than 0.05 in more than 10% of samples, probes containing single nucleotide polymorphisms (SNPs) at the CpG site, probes located on sex chromosomes, and cross-reactive probes as previously described (Capper et al., 2018; Chen et al., 2013).  Beta values for DNA methylation were calculated from normalised data using the minfi getBeta function.

label: Cy3 and Cy5

label_protocol: standard Illumina Protocols

extract_protocol: DNA extraction was performed on harvested cell pellets using the Maxwell® RSC Instrument (Promega) with either the Maxwell® RSC Cultured Cells DNA Kit (Cat# AS1620) or the  Maxwell® RSC Blood DNA Kit (Cat# AS1400) for fresh and frozen cell samples, and the Maxwell® RSC FFPE Plus DNA Purification Kit (Cat# AS1720) for paraformaldehyde (PFA)-fixed cell samples, with no difference in DNA methylation analysis quality observed. Extracted DNA quantities were measured using the Quantus system together with the “QuantiFluor® ONE dsDNA” kit (Promega).

value: iPSC NSC Day 1

tag: Sex

value: Male

value: iPSCs were seeded on Geltrex in Essential 8 with 10 µM Y-27632, then switched after 2 days to neural induction medium (DMEM/F12, B27, N2, L-glutamine, HEPES, 10 µM dorsomorphin, 10 µM SB431542) for 7 days with daily medium changes. Differentiation efficiency was assessed by FACS for PAX6, Nestin, SOX1, and SOX2, and samples with >85% expression were stored at -80 °C. Neural stem cells were subsequently derived from ectoderm by maintaining in the induction medium for 18 days with daily medium changes, and harvested at -80 °C.

tag: cohort

value: Surplus


title: BIHi005-A_Not_Classifiable_6

value: iPSC NSC Day 3


title: S61_HEK293-AQP4-EmGFP E5415A+AC biol rep 1

description:
Library name: S61
Column name in gene_count_preprocessed_mev_data_reindl.gct: S61


title: Normal_1_5_11_3

first: Lin

address: Shatai South Road

description: Sample 464

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: male

value: Normal


title: A549 cells,shYTHDF3_1,6h


title: BIHi001-B_Not_Classifiable_14

value: Neural Stem Cells Ectoderm Day 3


title: Normal_1_5_12_1

description: Sample 469

value: testis


title: S57_HA IC biol rep 3

description:
Library name: S57
Column name in gene_count_preprocessed_mev_data_reindl.gct: S57

source_name: human primary astrocyte

value: human primary astrocyte

value: astrocyte

value: wildtype


title: S59_HA biol rep 2

description:
Library name: S59
Column name in gene_count_preprocessed_mev_data_reindl.gct: S59


title: A549 cells,shYTHDF3_2,6h


title: S60_HA biol rep 3

description:
Library name: S60
Column name in gene_count_preprocessed_mev_data_reindl.gct: S60


title: mir156a/b/c/d, D13, FT, LD, EM-seq

city: Berkeley

last: Dai

institute: University of California, Berkeley

description:
Library name: mir156a/b/c/d_D13_FT_LD
150x 150

value: First true leaves

tag: seed stock

tag: background

value: grown under long day conditions (16h light/ 8 h dark)


title: BIHi005-A_iPSC_derived_Neural_Stem_Cells_2

tag: cell line

value: Neural Stem Cells Day 30


title: Normal_1_5_10_7

city: Guangzhou

last: Li

institute: Southern Medical University

description: Sample 460


title: A549 cells,shYTHDF3_2,0h


title: BIHi001-B_Not_Classifiable_13

value: Neural Stem Cells Ectoderm Day 1


title: Normal_1_5_11_1

description: Sample 462


title: Normal_1_5_10_8

description: Sample 461


title: S58_HA biol rep 1

description:
Library name: S58
Column name in gene_count_preprocessed_mev_data_reindl.gct: S58

tag: genotype


title: A549 cells,shYTHDF3_1,0h

value: A549 cell


title: Normal_1_5_10_3

description: Sample 458


title: A549 cells,shYTHDF3_3,0h


title: A549 cells,shContrl_2,6h


title: S54_HA AC biol rep 3

description:
Library name: S54
Column name in gene_count_preprocessed_mev_data_reindl.gct: S54

tag: treatment

value: active human complement


title: S56_HA IC biol rep 2

description:
Library name: S56
Column name in gene_count_preprocessed_mev_data_reindl.gct: S56

value: inactive human complement


title: Normal_1_5_10_6

description: Sample 459

tag: gender


title: UCSFi001-A_iPSC_derived_Mesoderm_1

value: Trilineage Mesoderm

value: Male

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.

value: Validation


title: BIHi005-A_iPSC_derived_Neural_Stem_Cells_1

value: Neural Stem Cells Day 18

value: iPSCs were seeded on Geltrex in Essential 8 with 10 µM Y-27632, then switched after 2 days to neural induction medium (DMEM/F12, B27, N2, L-glutamine, HEPES, 10 µM dorsomorphin, 10 µM SB431542) for 7 days with daily medium changes. Differentiation efficiency was assessed by FACS for PAX6, Nestin, SOX1, and SOX2, and samples with >85% expression were stored at -80 °C. Neural stem cells were subsequently derived from ectoderm by maintaining in the induction medium for 18 days with daily medium changes, and harvested at -80 °C.

value: Surplus


title: S53_HA AC biol rep 2

description:
Library name: S53
Column name in gene_count_preprocessed_mev_data_reindl.gct: S53

value: human primary astrocyte


title: BIHi287-A_iPSC_derived_Mesoderm_1


title: S52_HA AC biol rep 1

description:
Library name: S52
Column name in gene_count_preprocessed_mev_data_reindl.gct: S52

value: astrocyte


title: A549 cells,shContrl_3,6h


title: A549 cells,shContrl_1,6h


title: Normal_1_5_10_2

description: Sample 457

value: male

tag: age

value: Normal

value: testis


title: Normal_1_4_9_8

description: Sample 455

tag: condition


title: BIHi005A-SCB_iPSC_derived_Mesoderm_1


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_6

value: Neural Stem Cells Day 30


title: BIHi001-B-7_iPSC_derived_Mesoderm_1

value: Training


title: Normal_1_5_10_1

description: Sample 456

tag: testis


title: A549 cells,shControl_2,0h

value: A549 cell


title: S50_HA E5415A+IC biol rep 2

description:
Library name: S50
Column name in gene_count_preprocessed_mev_data_reindl.gct: S50

value: wildtype

value: anti-AQP4 antibody E5415A + inactive human complement


title: S55_HA IC biol rep 1

description:
Library name: S55
Column name in gene_count_preprocessed_mev_data_reindl.gct: S55

value: inactive human complement


title: BIHi001-B_iPSC_derived_Lung_6

value: Lung Progenitors Day 15

value: Male

value: iPSCs were adapted to mTeSR1 on Geltrex, seeded at 3×10⁶ cells/well in 6WP with 10 µM Y-27632, and differentiated using the STEMdiff Definitive Endoderm Kit (StemCell Technologies). At day 3, cells were assessed by FACS for CXCR4 (CD184) and SOX17, with cultures >90% efficiency stored at -80 °C or used for lung differentiation. For lung progenitors, day 3 endoderm cells were replated in cSFDM medium with 10 µM SB431542, 2 µM dorsomorphin, and 10 µM Y-27632, followed by anterior foregut induction (day 4–6) and subsequent lung induction medium (cSFDM + 3 µM CHIR, 10 ng/ml BMP4, 100 nM retinoic acid) until day 15. Lung progenitors were isolated by CPM expression using magnetic separation and stored as pellets at -80 °C.


title: A549 cells,shContrl_1,0h


title: Normal_1_4_9_6

description: Sample 453


title: S49_HA E5415A+IC biol rep 1

description:
Library name: S49
Column name in gene_count_preprocessed_mev_data_reindl.gct: S49


title: Normal_1_4_9_4

description: Sample 452


title: BIHi250-A_iPSC_derived_Lung_2

value: Female


title: KO_Caudal

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: KOC

data_processing:
Illumina NovaSeq-6000 for basecalling.
10x Genomics Cell Ranger pipeline (version 7.1.0) for barcoding, alignment, filtering.
Assembly: GRCh38-2020-A
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix.

source_name: Caudal halves of microfluidic neural tube-like structures

growth_protocol: Human pluripotent stem cells were seeded in a microfluidic channel. Designating the seeding day as day 0, extracellular matrix protein gel was overlaid on day 1 to form 3D tubular structures. The tissues were cultured in neural induction medium containing SB431542 and LDN193189. From day 2 to day 4, WNT activator CHIR99021 and retinoic acid gradients were applied to pattern the tissues rostrocaudally. Then the tissues were further cultured in neural induction medium until day 9 and dissociated for scRNAseq.

extract_protocol:
Microfluidic neural tube-like structures were dissociated into single cells using accutase. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v3).

treatment_protocol: The tissues were treated with SB431542 and LDN193189 for neural induction. They were further exposed to gradient of WNT activator CHIR99021 and retinoic acid for rostrocaudal patterning.

tag: tissue

value: Caudal neural progenitors

value: Neural tube rostrocaudal patterning


title: S48_HA E5415A+AC biol rep 3

description:
Library name: S48
Column name in gene_count_preprocessed_mev_data_reindl.gct: S48

value: human primary astrocyte

tag: cell type

value: anti-AQP4 antibody E5415A + active human complement


title: S51_HA E5415A+IC biol rep 3

description:
Library name: S51
Column name in gene_count_preprocessed_mev_data_reindl.gct: S51

value: astrocyte


title: Normal_1_4_9_3

description: Sample 451

value: male

value: Normal


title: KO_Rostral

description: KOR

source_name: Rostral halves of microfluidic neural tube-like structures

value: Rostral neural progenitors


title: S47_HA E5415A+AC biol rep 2

description:
Library name: S47
Column name in gene_count_preprocessed_mev_data_reindl.gct: S47


title: Normal_1_4_9_7

description: Sample 454

value: testis


title: A549 cells,shControl_3,0h

value: A549 cell


title: S46_HA E5415A+AC biol rep 1

description:
Library name: S46
Column name in gene_count_preprocessed_mev_data_reindl.gct: S46

value: wildtype


title: Normal_1_4_7_8

description: Sample 449


title: Normal_1_4_9_2

description: Sample 450


title: BCRTi005-A_iPSC_derived_Lung_1

value: Lung Progenitors Day 16

value: Validation


title: S30_U-87MG-ECFP-AQP4 biol rep 3

description:
Library name: S30
Column name in gene_count_preprocessed_mev_data_reindl.gct: S30

value: glioblastoma cell line


title: Normal_1_4_7_7

description: Sample 448


title: [RNA-Seq] HepAD38 shACSS2-3

city: Wuhan

first: jie

last: yang

address: No. 888 Gaoxin Avenue, Wuhan

institute: Wuhan IGENEBOOK Biotechnology Co.,Ltd

data_processing:
The adapter and low-quality reads were filtered out through cutadapt (version 1.11). Clean reads were mapped to the XXX reference genomes by Hisat2 (version 2.1.0), allowing up to two mismatches
Assembly: hg38
Supplementary files format and content: These genes were subjected to alignment against public protein databases;NR(RefSeq non-redundant proteins). Featurecount(v1.6.0) was used for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped)

source_name: Cell line

extract_protocol:
RNA-seq were performed by Wuhan IGENEBOOK Biotechnology Co.,Ltd (http://www.igenebook.com) . Briefly ,total RNA was extracted using the RNAprep Pure Kit DP432 (TIANGEN Biotech Co.,Ltd., Beijing, China), following the manufacturer’s instructions.
To construct RNA libraries with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina, 1 μg of total RNA was used

value: Cell line

value: HBV hepatoma cells


title: UCSFi001-A_iPSC_derived_Endothelial_cells_5

value: Endothelial cells Day 10

value: Male

value: iPSCs were differentiated to mesoderm and endothelial progenitors as in Patsch et al. (https://doi.org/10.1038/ncb3205). At day 0, cells were cultured in Endo Priming medium (DMEM/F12 + Neurobasal, B27–VitA, N2, β-mercaptoethanol, GlutaMAX, 6 µM CHIR, 25 ng/ml BMP4) for 72 h, followed by Endo Induction medium (StemPro-34, GlutaMAX, 200 ng/ml VEGF, 2 µM Forskolin) for 48 h. CD144+ cells were isolated as endothelial progenitors, and CD144– cells retained as pericyte progenitors. Endothelial progenitors were matured in EGM-2 (Lonza), with CD31/CD144 expression confirming endothelial identity (>90% CD31+), and all fractions were stored as pellets at -80 °C.


title: WT_Rostral

description: WTR

value: Rostral halves of microfluidic neural tube-like structures

value: NDE1+/+ (control)

value: Neural tube rostrocaudal patterning


title: UCSFi001-A_iPSC_derived_Lung_1

value: Lung Progenitors Day 15

value: iPSCs were adapted to mTeSR1 on Geltrex, seeded at 3×10⁶ cells/well in 6WP with 10 µM Y-27632, and differentiated using the STEMdiff Definitive Endoderm Kit (StemCell Technologies). At day 3, cells were assessed by FACS for CXCR4 (CD184) and SOX17, with cultures >90% efficiency stored at -80 °C or used for lung differentiation. For lung progenitors, day 3 endoderm cells were replated in cSFDM medium with 10 µM SB431542, 2 µM dorsomorphin, and 10 µM Y-27632, followed by anterior foregut induction (day 4–6) and subsequent lung induction medium (cSFDM + 3 µM CHIR, 10 ng/ml BMP4, 100 nM retinoic acid) until day 15. Lung progenitors were isolated by CPM expression using magnetic separation and stored as pellets at -80 °C.


title: Normal_1_4_7_6

description: Sample 447

value: male

value: Normal


title: UCSFi001-A_iPSC_derived_Endoderm_1

value: Lung Endoderm Day 3


title: [RNA-Seq] HepAD38 shACSS2-2


title: Normal_1_4_7_5

description: Sample 446

value: testis


title: S28_U-87MG-ECFP-AQP4 biol rep 1

description:
Library name: S28
Column name in gene_count_preprocessed_mev_data_reindl.gct: S28


title: [RNA-Seq] HepAD38 shACSS2-1


title: S27_U-87MG-ECFP-AQP4 IC biol rep 3

description:
Library name: S27
Column name in gene_count_preprocessed_mev_data_reindl.gct: S27

value: inactive human complement


title: BIHi250-A_iPSC_derived_Endoderm_3

value: Female

value: Validation


title: BIHi250-A_iPSC_derived_Lung_1

value: Lung Progenitors Day 14

value: Training


title: Normal_1_4_7_4

description: Sample 445


title: [RNA-Seq] HepAD38 shControl-3

value: Cell line

value: HBV hepatoma cells


title: BIHi296-B_iPSC_derived_Endoderm_1

value: Trilineage Endoderm

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.

value: Surplus


title: BIHi005-A_iPSC_derived_Lung_1

value: Male


title: BIHi287-A_iPSC_derived_Endoderm_1


title: WT_Caudal

description: WTC

value: Caudal halves of microfluidic neural tube-like structures

value: Caudal neural progenitors

value: NDE1+/+ (control)

value: Neural tube rostrocaudal patterning


title: S26_U-87MG-ECFP-AQP4 IC biol rep 2

description:
Library name: S26
Column name in gene_count_preprocessed_mev_data_reindl.gct: S26

value: glioblastoma cell line


title: Normal_1_4_7_3

description: Sample 444

value: male

value: Normal

value: testis


title: Normal_1_4_7_2

description: Sample 443


title: S29_U-87MG-ECFP-AQP4 biol rep 2

description:
Library name: S29
Column name in gene_count_preprocessed_mev_data_reindl.gct: S29


title: S24_U-87MG-ECFP-AQP4 AC biol rep 3

description:
Library name: S24
Column name in gene_count_preprocessed_mev_data_reindl.gct: S24

value: active human complement


title: S25_U-87MG-ECFP-AQP4 IC biol rep 1

description:
Library name: S25
Column name in gene_count_preprocessed_mev_data_reindl.gct: S25

value: inactive human complement


title: Normal_1_4_7_1

description: Sample 442


title: BIHi001-B-9_iPSC_derived_Endoderm_1


title: BIHi250-A_iPSC_derived_Endoderm_2

value: Female

value: Validation


title: S23_U-87MG-ECFP-AQP4 AC biol rep 2

description:
Library name: S23
Column name in gene_count_preprocessed_mev_data_reindl.gct: S23


title: HepAD38 shACSS2-3

data_processing:
Trimmomatic (version 0.38) was used to filter out low-quality reads. Clean reads were mapped to the genome by Bwa (version 0.7.15), allowing up to two mismatches. Samtools (version 1.3.1) was used to remove potential PCR duplicates, and MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth,300 bp; model fold, 5, 50;q value, 0.05). Wig files produced by MACS software were used for data visualization by IGV (version 2.3.91).
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&TAG

extract_protocol:
50000 cell was harvested and incubated with concanavalin A coated magnetic beads for 15 min at RT. Then, bead-bound cells was resuspended and incubated with the appropriate primary antibody (H3K27ac) overnight at 4℃. Afterwards,  secondary antibody was added to this mixture for 30 min at RT. The magnet stand was used to remove unbound antibodies.pA-Tn5 adapter complex was added at this step at RT for 1 h,then,remove unbound pA-Tn5 protein.Next,cells were resuspended in tagmentation buffer at 37℃ for 1 h. After that, immunoprecipitated DNA was saved.
Library was sequenced on Illumina novaseq 6000 with PE 150 method

value: Cell line

value: HBV hepatoma cells


title: HepAD38 shACSS2-2


title: BIHi001-B-13_iPSC_derived_Endoderm_1

value: Trilineage Endoderm

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.


title: S21_U-87MG-ECFP-AQP4 E5415A+IC biol rep 3

description:
Library name: S21
Column name in gene_count_preprocessed_mev_data_reindl.gct: S21

value: anti-AQP4 antibody E5415A + inactive human complement


title: [RNA-Seq] HepAD38 shControl-1


title: HepAD38 shACSS2-1


title: BIHi001-B-12_iPSC_derived_Endoderm_1

value: Male

value: Surplus


title: Normal_1_4_6_7

description: Sample 440


title: Normal_1_4_6_6

description: Sample 439


title: Normal_1_4_6_8

description: Sample 441


title: S20_U-87MG-ECFP-AQP4 E5415A+IC biol rep 2

description:
Library name: S20
Column name in gene_count_preprocessed_mev_data_reindl.gct: S20


title: Normal_1_4_6_4

description: Sample 438


title: [RNA-Seq] HepAD38 shControl-2


title: BIHi001-B-11_iPSC_derived_Endoderm_1


title: HepAD38 shControl-3


title: HepAD38 shControl-2


title: S19_U-87MG-ECFP-AQP4 E5415A+IC biol rep 1

description:
Library name: S19
Column name in gene_count_preprocessed_mev_data_reindl.gct: S19