title: Arid1a KO TE cells, d8 [D8_KO_TE_Exp2_Rep1]


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 1

status: Public on Jun 13 2023

type: SRA

city: Gif-sur-yvette

first: Matthieu

last: Gerard

address: Route Nationale

country: France

institute: CEA

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H3 (Abcam ab1791).
SMARCA4-AID_g7-8-9_rep1_H3_2020

library_source: genomic

data_processing:
Cleaning with fastp=0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 –overrepresentation_analysis --trim_poly_g
Alignment with bowtie2=2.4.2, default parameters
Marking duplicates reads with picard=2.23.8, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=STRICT
Filtring with samtools=1.11, parameters : -h -f 1 -F 3852 -q 30
Coverage with deeptools=3.5.0 (for the blacklist : http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz), parameters: bamCoverage --outFileFormat bigwig --binSize 1 --numberOfProcessors 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM --MNase --minFragmentLength 10 --extendReads --centerReads --maxFragmentLength 500 --ignoreForNormalization chrX chrY chrM --blackListFileName mm9-blacklist.bed.gz
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mus musculus ES cells were grown on mitomycin C-inactivated  Mus musculus embryonic fibroblasts at 37 °C, 5 % CO2, in DMEM (Sigma) supplemented by leukaemia inhibitory factor (LIF), 1X non-essential amino acids (Invitrogen), 15 % foetal calf serum (Invitrogen), 0.2 % β-mercaptoethanol (Sigma) and 1X penicillin/streptomycin (Invitrogen).

extract_protocol:
Chromatin preparation: ES cells were collected and fixed in D15 culture medium containing 1 % formaldehyde (Sigma) for 10 min at 20°C. We stopped fixation by adding glycine to 125 mM, and the cells were centrifugated and washed three times with PBS. Cells were then permeabilized in Tris-HCl pH 7.5 15 mM, NaCl 15 mM, MgCl2 5 mM, EGTA 0.1 mM, KCl 60 mM, Sucrose 0.3 M, 0.4% IGEPAL CA-630 (I3021, Sigma) during 15 min on ice. We next diluted the cells with two volumes of MNase buffer (Tris-HCl pH 7.5 20 mM, NaCl 20 mM, CaCl2 2 mM, MgCl2 4 mM, KCl 15 mM, 0.1 M sucrose), and chromatin was digested during 10 min at 37 °C with 6 Kunitz units of MNase (New England Biolabs, 200 Kunitz units/µl) per 1 million cells. We stopped MNase digestion by adding a final concentration of 10 mM EDTA. We released chromatin from MNase-treated ES cells by passing the cell suspension 13 times through a 26G syringe. Next, we centrifuged the samples, and the supernatants containing the solubilized chromatin were used directly for ChIP-seq experiments or sucrose gradient centrifugation.
DNA libraries were prepared using MicroPlex Library Preparation Kit v2 or v3 (Diagenode)

treatment_protocol: untreated

tag: cell line

tag: cell type

value: embryonic stem cells

tag: treatment

value: treated with auxin for 20 hours

tag: strain

tag: chip antibody

value: histone H3 (Abcam ab1791)


title: Arid1a Het MP cells, d8 [D8_Het_MP_Exp2_Rep3]

city: San Diego

first: Bryan

last: McDonald

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto"
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig, bed

source_name: Arid1a Het

extract_protocol:
Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.

value: Arid1a Het


title: R1-144hr-Dans

type: RNA

city: Baltimore

first: Kevin

last: Emmerich

state: MD

address: 400 N Broadway

department: Human Genetics

institute: Johns Hopkins University

description: NTR:Rod fish, 144h post Dan

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Bioconductor suite in the R statistical software, LIMMA, Carmaweb, and Microsoft Access were used for data processing, differential expression testing and storage

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: Transgenic rod fish after Dan treatment (control)

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were either treated with control Danieau's media or with 2.5 mM Mtz for 24h (unless collected earlier) to induce cell death of either rod or bipolar cells

tag: tissue

value: dissected eye

tag: sequencing replicate


title: R2-24hr-MTZ

description: NTR:Rod fish, 24h post mtz

source_name: Transgenic rod fish after mtz treatment (experimental condition)


title: Histone H2A MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g7-8-9_rep2_H2A_2020

value: untreated

value: histone H2A (Abcam ab18255)


title: Arid1a Het MP cells, d8 [D8_Het_MP_Exp2_Rep2]


title: R1-96hr-MTZ

description: NTR:Rod fish, 96h post mtz


title: R1-96hr-Dans

description: NTR:Rod fish, 96h post Dan


title: R1-72hr-MTZ

description: NTR:Rod fish, 72h post mtz


title: Arid1a Het MP cells, d8 [D8_Het_MP_Exp2_Rep1]


title: R1-60hr-MTZ

description: NTR:Rod fish, 60h post mtz


title: Arid1a Het EEC cells, d8 [D8_Het_EEC_Exp2_Rep3]


title: R1-860hr-Dans

description: NTR:Rod fish, 60h post Dan


title: Histone H2B MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2B (Abcam ab1790).
TIR1_g7-8-9_rep2_H2B_2020

value: histone H2B (Abcam ab1790)


title: R1-72hr-Dans

description: NTR:Rod fish, 72h post Dan


title: Histone H4 MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g7-8-9_rep2_H4_2020

value: histone H4 (Abcam ab7311)


title: R1-48hr-MTZ

description: NTR:Rod fish, 48h post mtz


title: R1-48hr-Dans

description: NTR:Rod fish, 48h post Dan


title: Arid1a Het EEC cells, d8 [D8_Het_EEC_Exp2_Rep2]


title: Histone H4 MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g7-8-9_rep1_H4_2020


title: R1-240hr-Dans

description: NTR:Rod fish, 240h post Dan


title: R1-40hr-MTZ

description: NTR:Rod fish, 40h post mtz


title: R1-40hr-Dans

description: NTR:Rod fish, 40h post Dan


title: R1-240hr-MTZ

description: NTR:Rod fish, 240h post mtz


title: Arid1a Het EEC cells, d8 [D8_Het_EEC_Exp2_Rep1]


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g7-8-9_rep2_H3_2020


title: R1-32hr-MTZ

description: NTR:Rod fish, 32h post mtz


title: R1-32hr-Dans

description: NTR:Rod fish, 32h post Dan


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g7-8-9_rep1_H3_2020


title: Arid1a Het TE cells, d8 [D8_Het_TE_Exp2_Rep3]


title: R1-24hr-MTZ

description: NTR:Rod fish, 24h post mtz


title: R1-24hr-Dans

description: NTR:Rod fish, 24h post Dan


title: R1-16hr-MTZ

description: NTR:Rod fish, 16h post mtz


title: Histone H2A MNase ChIP-seq medium sedimentation rate (7-8-9) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g7-8-9_rep1_H2A_2020


title: Arid1a Het TE cells, d8 [D8_Het_TE_Exp2_Rep2]


title: R1-16hr-Dans

description: NTR:Rod fish, 16h post Dan


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7 and 8) was performed using antibodies against histone H3 (Abcam ab1791).
ChIP_H3_grad2_f7-8_200128


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7 and 8) was performed using antibodies against histone H3 (Abcam ab1791).
ChIP_H3_grad1_f7-8_200128


title: R1-8hr-MTZ

description: NTR:Rod fish, 8h post mtz


title: Arid1a Het TE cells, d8 [D8_Het_TE_Exp2_Rep1]


title: R1-8hr-Dans

description: NTR:Rod fish, 8h post Dan


title: WT MP cells, d8 [D8_WT_MP_Exp2_Rep3]

source_name: WT

value: WT


title: Histone H2A MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2A (Abcam ab18255).
SMARCA4-AID_g5-6_rep2_H2A_2020


title: R1-0hr

description: NTR:Rod fish, 0h post mtz

source_name: Transgenic rod fish before ablation


title: WT MP cells, d8 [D8_WT_MP_Exp2_Rep2]


title: Histone H2A MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2A (Abcam ab18255).
SMARCA4-AID_g5-6_rep1_H2A_2020


title: BP Run3 MTZ 240 (C7)

description: NTR:Bipolar fish, 240h post mtz

source_name: Transgenic bipolar fish after mtz treatment (experimental condition)


title: WT MP cells, d8 [D8_WT_MP_Exp2_Rep1]


title: BP Run3 Dan 096 (C7)

description: NTR:Bipolar fish, 96h post Dan

source_name: Transgenic bipolar fish after Dan treatment (control)


title: Histone H2B MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2B (Abcam ab1790).
SMARCA4-AID_g5-6_rep2_H2B_2020


title: BP Run3 MTZ 144 (C7)

description: NTR:Bipolar fish, 144h post mtz


title: BP Run3 Dan 144 (C7)

description: NTR:Bipolar fish, 144h post Dan


title: Histone H2B MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2B (Abcam ab1790).
SMARCA4-AID_g5-6_rep1_H2B_2020


title: BP Run3 MTZ 072 (C7)

description: NTR:Bipolar fish, 72h post mtz


title: BP Run3 MTZ 096 (C7)

description: NTR:Bipolar fish, 96h post mtz


title: WT EEC cells, d8 [D8_WT_EEC_Exp2_Rep2]


title: WT EEC cells, d8 [D8_WT_EEC_Exp2_Rep3]


title: BP Run3 Dan 072 (C7)

description: NTR:Bipolar fish, 72h post Dan


title: Histone H4 MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H4 (Abcam ab7311).
SMARCA4-AID_g5-6_rep2_H4_2020


title: WT EEC cells, d8 [D8_WT_EEC_Exp2_Rep1]


title: BP Run3 MTZ 060 (C7)

description: NTR:Bipolar fish, 60h post mtz


title: BP Run3 Dan 060 (C7)

description: NTR:Bipolar fish, 60h post Dan


title: Histone H4 MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H4 (Abcam ab7311).
SMARCA4-AID_g5-6_rep1_H4_2020


title: WT TE cells, d8 [D8_WT_TE_Exp2_Rep3]


title: BP Run3 MTZ 048 (C7)

description: NTR:Bipolar fish, 48h post mtz


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
SMARCA4-AID_g5-6_rep2_H3_2020


title: BP Run3 MTZ 040 (C7)

description: NTR:Bipolar fish, 40h post mtz


title: WT TE cells, d8 [D8_WT_TE_Exp2_Rep2]


title: BP Run3 Dan 048 (C7)

description: NTR:Bipolar fish, 48h post Dan


title: BP Run3 Dan 240 (C7)

description: NTR:Bipolar fish, 240h post Dan


title: BP Run3 Dan 040 (C7)

description: NTR:Bipolar fish, 40h post Dan


title: BP Run3 MTZ 032 (C7)

description: NTR:Bipolar fish, 32h post mtz


title: WT TE cells, d8 [D8_WT_TE_Exp2_Rep1]


title: Histone H2A MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g5-6_rep2_H2A_2020


title: BP Run3 Dan 032 (C7)

description: NTR:Bipolar fish, 32h post Dan


title: Arid1a KO MP cells, d8 [D8_KO_MP_Exp1_Rep2]

source_name: Arid1a KO

value: Arid1a KO


title: BP Run3 Dan 024 (C7)

description: NTR:Bipolar fish, 24h post Dan


title: BP Run3 MTZ 016 (C7)

description: NTR:Bipolar fish, 16h post mtz


title: BP Run3 MTZ 024 (C7)

description: NTR:Bipolar fish, 24h post mtz


title: Arid1a KO MP cells, d8 [D8_KO_MP_Exp1_Rep1]


title: Histone H2A MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g5-6_rep1_H2A_2020


title: BP Run3 Dan 016 (C7)

description: NTR:Bipolar fish, 16h post Dan


title: Histone H2B MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2B (Abcam ab1790).
TIR1_g5-6_rep2_H2B_2020


title: Arid1a KO EEC cells, d8 [D8_KO_EEC_Exp1_Rep2]


title: BP Run3 MTZ 008 (C7)

description: NTR:Bipolar fish, 8h post mtz


title: Arid1a KO EEC cells, d8 [D8_KO_EEC_Exp1_Rep1]


title: Histone H4 MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g5-6_rep2_H4_2020


title: BP Run3 Dan 008 (C7)

description: NTR:Bipolar fish, 8h post Dan


title: BP Run3 00 (C7)

description: NTR:Bipolar fish, 0h post mtz

source_name: Transgenic bipolar fish before ablation


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
SMARCA4-AID_g5-6_rep1_H3_2020


title: Histone H4 MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g5-6_rep1_H4_2020


title: BP Run2 MTZ 240 (C6)

description: NTR:Bipolar fish, 240h post mtz


title: Histone H2B MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H2B (Abcam ab1790).
TIR1_g5-6_rep1_H2B_2020


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g5-6_rep2_H3_2020


title: Arid1a KO TE cells, d8 [D8_KO_TE_Exp1_Rep1]


title: BP Run2 Dan 240 (C6)

description: NTR:Bipolar fish, 240h post Dan


title: Arid1a KO TE cells, d8 [D8_KO_TE_Exp1_Rep2]


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g5-6_rep1_H3_2020


title: BP Run2 MTZ 144 (C6)

description: NTR:Bipolar fish, 144h post mtz


title: Tbet KO MP cells, d8 [D8_TbetKO_MP_Exp1_Rep2]

source_name: Tbet KO

value: Tbet KO


title: Tbet KO MP cells, d8 [D8_TbetKO_MP_Exp1_Rep1]


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad2_f5-6_200727


title: Tbet KO EEC cells, d8 [D8_TbetKO_EEC_Exp1_Rep2]


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad1_f5-6_280120


title: BP Run2 MTZ 096 (C6)

description: NTR:Bipolar fish, 96h post mtz


title: SAMR1 4 brainstem

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: SAMR1 brainstem

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: brainstem

tag: age

tag: Sex

value: male


title: SAMR1 5 brainstem


title: Tbet KO EEC cells, d8 [D8_TbetKO_EEC_Exp1_Rep1]


title: SAMR1 2 brainstem


title: Histone H2A MNase ChIP-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g2-3-4_rep2_H2A_2020


title: SAMR1 3 brainstem


title: BP Run2 Dan 096 (C6)

description: NTR:Bipolar fish, 96h post Dan


title: Tbet KO TE cells, d8 [D8_TbetKO_TE_Exp1_Rep2]


title: SAMP8 4 brainstem

source_name: SAMP8 brainstem


title: SAMP8 5 brainstem


title: Histone H2A MNase ChIP-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H2A (Abcam ab18255).
TIR1_g2-3-4_rep1_H2A_2020


title: BP Run2 MTZ 072 (C6)

description: NTR:Bipolar fish, 72h post mtz


title: BP Run2 Dan 072 (C6)

description: NTR:Bipolar fish, 72h post Dan


title: WT MP cells, d8 [D8_WT_MP_Exp1_Rep2]


title: Histone H2B MNase ChIP-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H2B (Abcam ab1790).
TIR1_g2-3-4_rep2_H2B_2020


title: Histone H2B MNase ChIP-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H2B (Abcam ab1790).
TIR1_g2-3-4_rep1_H2B_2020


title: SAMP8 2 brainstem


title: BP Run2 Dan 144 (C6)

description: NTR:Bipolar fish, 144h post Dan


title: WT MP cells, d8 [D8_WT_MP_Exp1_Rep1]


title: SAMP8 3 brainstem


title: BP Run2 Dan 060 (C6)

description: NTR:Bipolar fish, 60h post Dan


title: Histone H4 MNase ChIP-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g2-3-4_rep2_H4_2020


title: BP Run2 MTZ 060 (C6)

description: NTR:Bipolar fish, 60h post mtz


title: SAMR1 1 brainstem


title: WT EEC cells, d8 [D8_WT_EEC_Exp1_Rep2]


title: SAMP8 1 brainstem


title: WT EEC cells, d8 [D8_WT_EEC_Exp1_Rep1]


title: Histone H3 MNase ChIP-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g2-3-4_rep2_H3_2020


title: BP Run2 Dan 048 (C6)

description: NTR:Bipolar fish, 48h post Dan


title: WT TE cells, d8 [D8_WT_TE_Exp1_Rep2]


title: SAMR1 4 cortex

source_name: SAMR1 cortex

value: cortex


title: Tbet KO TE cells, d8 [D8_TbetKO_TE_Exp1_Rep1]


title: BP Run2 MTZ 040 (C6)

description: NTR:Bipolar fish, 40h post mtz


title: SAMR1 3 cottex


title: Histone H3 MNase ChIP-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H3 (Abcam ab1791).
TIR1_g2-3-4_rep1_H3_2020


title: WT TE cells, d8 [D8_WT_TE_Exp1_Rep1]


title: Histone H3 MNase ChIP-seq top of gradient (3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 3 and 4) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad2_f3-4_200727


title: BP Run2 Dan 040 (C6)

description: NTR:Bipolar fish, 40h post Dan


title: KO cells, d5 [D5_KO_Rep2]


title: Histone H3 MNase ChIP-seq top of gradient (3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 3 and 4) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad1_f3-4_280120


title: BP Run2 MTZ 032 (C6)

description: NTR:Bipolar fish, 32h post mtz


title: SAMR1 1 cortex


title: KO cells, d5 [D5_KO_Rep1]


title: BP Run2 MTZ 048 (C6)

description: NTR:Bipolar fish, 48h post mtz


title: Histone H4 MNase ChIP-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against histone H4 (Abcam ab7311).
TIR1_g2-3-4_rep1_H4_2020


title: SAMR1 5 cortex


title: WT cells, d5 [D5_WT_Rep2]


title: PCL3 (iPSC cultured on PCL soft substrate)

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

library_source: transcriptomic

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol:
IPSCs were derived from BJ-2522 human neonatal foreskin fibroblast cells (ATCC) by transfecting the cells with OCT4,SOX2andKLF4retroviruses
The iPSCs were maintained on Geltrex®-coated (Life Technologies) tissue culture plates in mTeSR1 growth media (StemCell Technologies) and seeded onto the PCL substrates at a cell density of approximately 120,000 cells per cm2. A ROCK inhibitor, Y-27632 (10 μM, Sigma Aldrich), was supplemented into the media to improve initial cell attachment and survival. The following day, Y-27632 was removed from the media.

extract_protocol: Total RNA from the iPSCs grown in either plastic (Control) or PCL substrats was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction. cDNA libraries were then prepared using the KAPA RNA Hyperprep Kit with RiboErase (HMR)

treatment_protocol: iPSCs were cultured on plastic tissue culture plates or PCL substrates

value: iPSCs derived from BJ-2522 cells

value: cultured on PCL soft substrate


title: BP Run2 Dan 032 (C6)

description: NTR:Bipolar fish, 32h post Dan


title: BP Run2 MTZ 024 (C6)

description: NTR:Bipolar fish, 24h post mtz


title: PCL2 (iPSC cultured on PCL soft substrate)


title: WT cells, d5 [D5_WT_Rep1]


title: SAMP8 5 cortex

source_name: SAMP8 cortex


title: BP Run2 Dan 024 (C6)

description: NTR:Bipolar fish, 24h post Dan


title: Arid1a KO cells, d3 [D3_KO_Rep2]


title: SAMP8 4 cortex


title: BP Run2 MTZ 016 (C6)

description: NTR:Bipolar fish, 16h post mtz


title: PCL1 (iPSC cultured on PCL soft substrate)


title: SAMP8 3 cortex


title: SAMP8 2 cortex


title: CTRL4 (iPSC cultured on plastic plate)

value: cultured on plastic plate


title: SAMR1 2 cortex


title: BP Run2 Dan 016 (C6)

description: NTR:Bipolar fish, 16h post Dan


title: Arid1a KO cells, d3 [D3_KO_Rep1]


title: SAMP8 1 cortex


title: WT cells, d3 [D3_WT_Rep2]


title: PCL4 (iPSC cultured on PCL soft substrate)


title: CTRL3 (iPSC cultured on plastic plate)


title: BP Run2 MTZ 008 (C6)

description: NTR:Bipolar fish, 8h post mtz


title: SAMR1 4 hippocampus

source_name: SAMR1 hippocampus

value: hippocampus


title: WT cells, d3 [D3_WT_Rep1]


title: BP Run2 Dan 008 (C6)

description: NTR:Bipolar fish, 8h post Dan


title: CTRL2 (iPSC cultured on plastic plate)


title: SAMR1 5 hippocampus


title: WT cells, 48h activated in vitro [48h_WT_Rep2]


title: SAMR1 3 hippocampus


title: WT cells, 48h activated in vitro [48h_WT_Rep1]


title: BP Run1 MTZ 240 (C3)

description: NTR:Bipolar fish, 240h post mtz


title: NC_PBMC

city: Shenzhen

first: Cantong

last: Zhang

address: 1017 Dongmen North Road, Luohu District, Shenzhen, China

country: China

institute: Shenzhen's hospital

data_processing:
Barcode processing: To improve data quality, a ‘whitelist’ of correct barcode sequences was applied to fix the occasional sequencing error in barcodes obtained from the ‘I2’ index read
Genome alignment: Reference-based analysis was performed using the Cell Ranger ATAC pipeline. BWA-MEM was applied with default parameters to align the trimmed read pairs that were greater than 25 bp to GRCh38
Filteing: We filtered scATAC-seq data using cut-offs of 1,000 unique nuclear fragments per cell and a transcription start site (TSS) enrichment score of 8 to exclude low-quality cells in 10x genomic Cell Ranger ATAC platform
Peak calling: First, the number of transposition events at each base pair along the genome was counted. Next, a smoothed profile of these events with a 401 bp moving window around each base pair and fitting a ZINBA-like mixture model was generated. Then, a signal threshold was set to determine whether a region was a peak signal or noise based on an odds ratio of 1/5. Finally, peaks within 500 bp of each other were merged to produce a position-sorted BED file.
Cell calling and peak-barcode matrix: For each barcode, the mapped high-quality fragments that passed all filters were recorded, and the number of fragments that overlapped any peak regions was used to separate the signal from noise. To capture the signal and noise, a mixture model of two negative binomial distributions was set, and barcodes that corresponded to real cells from the non-cell barcodes were separated by setting an odds ratio of 1000. Subsequently, a raw peak-barcode matrix consisting of the counts of fragment ends within each peak region for each barcode was produced. After filtering to contain only cell barcodes, the matrix was used in subsequent analyses, such as dimensionality reduction, clustering and visualization.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files for barcodes; mtx files for matrix; bed files for peaks

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were separated using an equal proportion of Ficoll-Paque Plus. Nuclei suspensions were obtained by adding lysis buffer (10 mM Tris-HCl, 3 mM MgCl2, 10 mM NaCl , 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 1% BSA). The final libraries were constructed via PCR with P5 and P7 primers in Illumina® bridge amplification.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10x GENOMICS)

value: peripheral blood

value: PBMCs

tag: disease state

value: Healthy controls


title: SAMR1 2 hippocampus


title: BP Run1 Dan 240 (C3)

description: NTR:Bipolar fish, 240h post Dan

value: dissected eye


title: CTRL1 (iPSC cultured on plastic plate)


title: BP Run2 00 (C6)

description: NTR:Bipolar fish, 0h post mtz


title: BP Run1 MTZ 144 (C3)

description: NTR:Bipolar fish, 144h post mtz


title: WT cells, Naive [Naive_WT_Rep1]


title: SAMR1 1 hippocampus


title: D8_KO_MP_Rep2

description:
d8/bam/mm39/KO_MP2_S15_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

data_processing:
Sequence reads were aligned to GRCm39 (mm39) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using featureCounts (-s 0) with GENCODE M27 annotation
Assembly: GRCm39 (mm39)
Supplementary files format and content: featureCounts.d3.mm39.vM27.txt
Supplementary files format and content: featureCounts.d5.mm39.vM27.WT.txt
Supplementary files format and content: featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a KO MP cells, d8

extract_protocol:
RNA was harvested using Rneasy Plus Micro kit (Qiagen) and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA kit following manufacturer's protocols.
RNA-seq 51bp single-end sequencing

tag: genotype

tag: time

value: Day 8

tag: infection

value: LCMV Armstrong


title: BP Run1 Dan 144 (C3)

description: NTR:Bipolar fish, 144h post Dan


title: D8_KO_MP_Rep1

description:
d8/bam/mm39/KO_MP1_S14_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: RA_PBMC

value: Rheumatoid arthritis


title: SAMP8 4 hippocampus

source_name: SAMP8 hippocampus


title: SAMP8 5 hippocampus


title: D8_KO_EEC_Rep3

description:
d8/bam/mm39/KO_EEC3_S23_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a KO EEC cells, d8


title: BP Run1 Dan 096 (C3)

description: NTR:Bipolar fish, 96h post Dan


title: SAMP8 3 hippocampus


title: D8_KO_EEC_Rep2

description:
d8/bam/mm39/KO_EEC2_S22_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: SAMP8 2 hippocampus


title: WT cells, Naive [Naive_WT_Rep2]

value: WT


title: IL-23-Th17 Veh 3

city: Winston-Salem

first: Qianqian

last: Song

state: NC

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2
We used featureCounts to collect the raw gene count information with the following configurations -t exon -g gene_name.
Assembly: mm10
Supplementary files format and content: tab-delimited files with gene names in column one and counts in the second column.

source_name: Polarized CD4+ Splenocytes

extract_protocol: mRNA was isolated from harvested differentiated cells using mRNeasy extraction kit (Qiagen) following the manufacturer's protocol. Purified mRNA was submitted for library construction and NGS sequencing by BGI commercial NGS services.

treatment_protocol: 24-well tissue culture plates were coated with 200 ng/ml rabbit a-hamster IgG over night at 4°C. Spleens were homogenized through a 40 mm cell strainer and resuspended in their appropriate differentiation conditions (homeostatic Th17 – 20 ng/ml IL-6, 2.5 ng/ml TGF-b; IL23-Th17 – 20 ng/ml IL-6, 20 ng/ml IL-23, 20 ng/ml IL-1b, 1 μg/ml aIFN-g with both conditions containing 250 ng/ml aCD-3e and 1 mg/ml aCD-28) in IMDM containing 10% FBS, 50 mM b-mercaptoethanol, 1X antibiotics/antimycotics, pre-supplemented with L-glutamine and HEPES. Coating antibody was washed from 24-well plate and cells were seeded at 400,000 cells per well in 2 ml of differentiation media containing 0.4 uM CLF or DMSO vehicle control. Cells were left to differentiate for 72 hours at 37°C until harvested for downstream analyses.

tag: polarized subset

value: Inflammatory Th17

value: DMSO

value: 8 weeks


title: BP Run1 MTZ 072 (C3)

description: NTR:Bipolar fish, 72h post mtz


title: SAMP8 1 hippocampus

value: male


title: Jurkat miR-93 -/- #2 IP fraction Ago2 replicate 2

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

country: Germany

institute: Charité - Universitätsmedizin

description: immunoprecipitated fraction

hyb_protocol: Hybridization was performed using the GeneChip™ Hybridization, Wash, and Stain Kit (Cat# 900720) according to the manufacturers instructions.

scan_protocol: Relative signal intensities were extracted using Affymetrix feature extraction software version 1.1.0.1567.

data_processing: The CEL files, generated from Affymetrix RNA microarray image analysis software, were processed through Transcriptome Analysis Console 4.0 which normalizes (and applies the log2 function to) array signals using a robust multiarray averaging algorithm.

source_name: miR-93 knockout cells #2

label_protocol: Labelling was performed using the GeneChip™ WT Terminal Labeling Kit (Cat# 900670) according to the manufacturers instructions.

growth_protocol: Jurkat clones were cultured in RPMI-1640 containing 10% FCS and penicillin/streptomycin at 37°C in 5% CO2 incubator

extract_protocol: RNA was extracted using the miRNeasy mini (input fraction) or micro (IP fraction) kit (Qiagen, Cat# 217004 and 217084, respectively) according to the manufacturer’s instructions. RNA quality was assessed using Agilent bioanalyzer 2100 using Eukaryote Total RNA Nano assay version 2.6.

treatment_protocol: CRISPR-Cas9 mediated knockout of miR-93 was performed. Controls included a CRISPR-treated, but unedited control as well as the parental cells.

value: Jurkat


title: D8_KO_EEC_Rep1

description:
d8/bam/mm39/KO_EEC1_S21_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

value: Arid1a KO


title: Jurkat miR-93 -/- #2 IP fraction IgG replicate 2

description: immunoprecipitated fraction


title: BP Run1 MTZ 0060 (C3)

description: NTR:Bipolar fish, 60h post mtz


title: D8_KO_TE_Rep2

description:
d8/bam/mm39/KO_TE2_S8_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a KO TE cells, d8


title: IL-23-Th17 Veh 2


title: BP Run1 Dan 0072 (C3)

description: NTR:Bipolar fish, 72h post Dan


title: D8_KO_TE_Rep1

description:
d8/bam/mm39/KO_TE1_S7_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: IL-23-Th17 Veh 1


title: BP Run1 MTZ 096 (C3)

description: NTR:Bipolar fish, 96h post mtz

source_name: Transgenic bipolar fish after mtz treatment (experimental condition)


title: IL-23-Th17 CLF 3

value: CLF


title: BP Run1 Dan 060 (C3)

description: NTR:Bipolar fish, 60h post Dan

source_name: Transgenic bipolar fish after Dan treatment (control)


title: Jurkat miR-93 -/- #1 IP fraction IgG replicate 2

description: immunoprecipitated fraction

source_name: miR-93 knockout cells #1


title: Jurkat miR-93 +/+ control IP fraction Ago2 replicate 2

description: immunoprecipitated fraction

source_name: CRISPR control cells


title: D8_Het_MP_Rep3

description:
d8/bam/mm39/Het_MP3_S13_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a Het MP cells, d8

value: Arid1a Het


title: IL-23-Th17 CLF 1


title: D8_Het_MP_Rep2

description:
d8/bam/mm39/Het_MP2_S12_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Homeostatic Th17 Veh 3

value: Homeostatic Th17


title: D8_Het_MP_Rep1

description:
d8/bam/mm39/Het_MP1_S11_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Jurkat parental IP fraction IgG replicate 2

description: immunoprecipitated fraction

source_name: Parental cells


title: BP Run1 MTZ 040 (C3)

description: NTR:Bipolar fish, 40h post mtz


title: BP Run1 Dan 048 (C3)

description: NTR:Bipolar fish, 48h post Dan


title: Jurkat miR-93 -/- #1 IP fraction Ago2 replicate 2

description: immunoprecipitated fraction


title: Jurkat miR-93 -/- #2 IP fraction Ago2 replicate 1

description: immunoprecipitated fraction


title: Homeostatic Th17 Veh 2


title: D8_Het_EEC_Rep3

description:
d8/bam/mm39/Het_EEC3_S20_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a Het EEC cells, d8


title: BP Run1 Dan 040 (C3)

description: NTR:Bipolar fish, 40h post Dan


title: BP Run1 MTZ 032 (C3)

description: NTR:Bipolar fish, 32h post mtz


title: D8_Het_EEC_Rep2

description:
d8/bam/mm39/Het_EEC2_S19_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: BP Run1 Dan 032 (C3)

description: NTR:Bipolar fish, 32h post Dan


title: IL-23-Th17 CLF 2


title: Jurkat parental IP fraction Ago2 replicate 2

description: immunoprecipitated fraction


title: Jurkat miR-93 +/+ control IP fraction IgG replicate 2

description: immunoprecipitated fraction


title: D8_Het_TE_Rep3

description:
d8/bam/mm39/Het_TE3_S6_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: Arid1a Het TE cells, d8


title: Homeostatic Th17 CLF 2


title: Homeostatic Th17 CLF 3


title: Homeostatic Th17 Veh 1


title: D8_Het_EEC_Rep1

description:
d8/bam/mm39/Het_EEC1_S18_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Jurkat miR-93 -/- #2 IP fraction IgG replicate 1

description: immunoprecipitated fraction


title: BP Run1 MTZ 048 (C3)

description: NTR:Bipolar fish, 48h post mtz


title: Jurkat miR-93 -/- #1 IP fraction IgG replicate 1

description: immunoprecipitated fraction


title: Jurkat miR-93 -/- #1 IP fraction Ago2 replicate 1

description: immunoprecipitated fraction


title: BP Run1 MTZ 024 (C3)

description: NTR:Bipolar fish, 24h post mtz


title: D8_Het_TE_Rep2

description:
d8/bam/mm39/Het_TE2_S5_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Jurkat miR-93 +/+ control IP fraction Ago2 replicate 1

description: immunoprecipitated fraction


title: Homeostatic Th17 CLF 1


title: BP Run1 Dan 024 (C3)

description: NTR:Bipolar fish, 24h post Dan


title: D8_Het_TE_Rep1

description:
d8/bam/mm39/Het_TE1_S4_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Jurkat miR-93 +/+ control IP fraction IgG replicate 1

description: immunoprecipitated fraction


title: Caput, 10% EtOH, Cessation, EM63

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

description: Illumina HiSeq sequencing of 20Mpair reads

data_processing:
Fast QC
Trimmomatic
Fast QC
RNA STAR
featureCounts
Assembly: GRCm39/mm39
Supplementary files format and content: featureCounts

source_name: caput

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Control, 6 EtOH%, or 10% EtOH

value: caput

value: 10% EtOH-Cessation


title: BP Run1 MTZ 016 (C3)

description: NTR:Bipolar fish, 16h post mtz


title: D8_WT_MP_Rep2

description:
d8/bam/mm39/WT_MP2_S10_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: WT MP cells, d8


title: Jurkat parental IP fraction IgG replicate 1

description: immunoprecipitated fraction


title: Caput, 10% EtOH, Cessation, EM49


title: BP Run1 Dan 016 (C3)

description: NTR:Bipolar fish, 16h post Dan


title: D8_WT_MP_Rep1

description:
d8/bam/mm39/WT_MP1_S9_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: BP Run1 Dan 008 (C3)

description: NTR:Bipolar fish, 8h post Dan


title: D8_WT_EEC_Rep2

description:
d8/bam/mm39/WT_EEC2_S17_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: WT EEC cells, d8


title: D8_WT_EEC_Rep1

description:
d8/bam/mm39/WT_EEC1_S16_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt


title: Jurkat miR-93 -/- #2 total fraction Ago2 replicate 2

description: total fraction (= input)


title: Jurkat miR-93 -/- #2 total fraction IgG replicate 2

description: total fraction (= input)


title: Caput, 6% EtOH, Cessation, M2120

value: 6% EtOH-Cessation


title: Caput, 6% EtOH, Cessation, M2118


title: BP Run1 MTZ 008 (C3)

description: NTR:Bipolar fish, 8h post mtz

value: dissected eye


title: Jurkat parental IP fraction Ago2 replicate 1

description: immunoprecipitated fraction


title: D8_WT_TE_Rep2

description:
d8/bam/mm39/WT_TE3_S3_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

source_name: WT TE cells, d8

value: Day 8


title: Jurkat miR-93 -/- #1 total fraction Ago2 replicate 2

description: total fraction (= input)


title: Dataset 2: NMuMG replicate #2

city: Charleston

first: William

middle: Scott

last: Streitfeld

state: SC

address: 173 Ashley Ave BSB 510

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
MME-R2_S18
Processed Dataset 2 - NMuMG vs NMuMG shPCBP1.txt

data_processing:
Files containing paired-end reads (.fastq.gz format) were uploaded into the Partek Flow web-based software platform (version 10.0.21).
For dataset 1: reads were trimmed then aligned to the GRCm38 (mm10) mouse genome assembly using the Bowtie2 applet. Aligned reads were annotated and gene counts were filtered by a predetermined threshold then normalized to the total number of reads for each sample. Processed values are shown as normalized counts per million reads.
For dataset 1: differential expression analysis was later calculated using the DESeq applet.
For dataset 2: Processed values are shown as normalized counts per million reads. Differential expression was identified by calculating the fold change (FC) relative to NMuMG untreated cells, by dividing the normalized counts for NMuMG shPCBP1 by the normalized counts for NMuMG untreated.
Assembly: mm10
Supplementary files format and content: Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt = tab delimited text values derived from a matrix (from MS Excel), containing normalized counts per million reads, for each protein coding gene detected, for each sample.
Supplementary files format and content: Processed Dataset 2 - NMuMG vs NMuMG shPCBP1.txt = tab delimited text values derived from a matrix (from MS Excel), containing normalized counts per million reads, for each protein coding gene detected, for each sample.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted from cells using simplyRNA Cells kit (cat # AS1390) with a Maxwell RSC 16 (Promega) according to the manufacturer’s specifications.  RNA QC, along with that of downstream libraries (below), was performed with a 4200 TapeStation (Agilent).
1 mg of total RNA was used for the construction of libraries with the New England Biolabs NEBNext® rRNA Depletion Kit (Cat# E6310X) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions.
Dual-indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 50 million paired-end 150 bp reads per library.

value: Mammary gland

value: NMuMG

value: Epithelial

value: Wild type


title: D8_WT_TE_Rep1

description:
d8/bam/mm39/WT_TE2_S2_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt

value: WT

value: LCMV Armstrong


title: BP Run1 00 (C3)

description: NTR:Bipolar fish, 0h post mtz

source_name: Transgenic bipolar fish before ablation


title: D5_WT_Rep3

description:
d5/bam/mm39/d5BM_WT3_S75_R1_001.mm39.bam
featureCounts.d5.mm39.vM27.WT.txt

source_name: WT cells, d5

value: Day 5


title: Dataset 2: NMuMG replicate #1

description:
MME-R1_S17
Processed Dataset 2 - NMuMG vs NMuMG shPCBP1.txt


title: Caput, Control, Cessation, CM33

value: Control-Cessation


title: Jurkat miR-93 -/- #1 total fraction IgG replicate 2

description: total fraction (= input)

value: Jurkat


title: Jurkat miR-93 +/+ control total fraction Ago2 replicate 2

description: total fraction (= input)


title: Caput, 10% EtOH, Cessation, EM42


title: Dataset 2: NMuMG shPCBP1 replicate #2

description:
E1KD-R2_S20
Processed Dataset 2 - NMuMG vs NMuMG shPCBP1.txt

value: shRNA knockdown of PCBP1


title: D5_WT_Rep2

description:
d5/bam/mm39/d5BM_WT2_S74_R1_001.mm39.bam
featureCounts.d5.mm39.vM27.WT.txt


title: Caput, Control, Cessation, CM24


title: Dataset 2: NMuMG shPCBP1 replicate #1

description:
E1KD-R1_S19
Processed Dataset 2 - NMuMG vs NMuMG shPCBP1.txt


title: D5_WT_Rep1

description:
d5/bam/mm39/d5BM_WT1_S73_R1_001.mm39.bam
featureCounts.d5.mm39.vM27.WT.txt


title: Dataset 1: NMuMG shPCBP1 LIFR KO cell line clone #2

description:
5107-MR-59_9_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: LIFR -/-

value: shRNA knockdown of PCBP1, CRISPR KO of LIFR


title: Caput, 6% EtOH, Cessation, M2112

value: caput


title: D3_KO_Rep3

description:
d3/bam/mm39/BM_D3_KO3_S5_R1_001.bam
featureCounts.d3.mm39.vM27.txt

source_name: Arid1a KO cells, d3

value: Arid1a KO

value: Day 3


title: Caput, 10% EtOH, 10 weeks, H8

value: 10% EtOH


title: Dataset 1: NMuMG shPCBP1 LIFR KO cell line clone #1

description:
5107-MR-59_8_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt


title: Caput, 10% EtOH, 10 weeks, EM10

description: Illumina HiSeq sequencing of 20Mpair reads


title: Dataset 1: NMuMG shPCBP1 FAM3C KO cell line clone #3

description:
5107-MR-59_7_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: FAM3C -/-

value: shRNA knockdown of PCBP1, CRISPR KO of FAM3C


title: Jurkat miR-93 +/+ control total fraction IgG replicate 2

description: total fraction (= input)


title: D3_KO_Rep2

description:
d3/bam/mm39/BM_D3_KO2_S4_R1_001.bam
featureCounts.d3.mm39.vM27.txt


title: Caput, 6% EtOH, 10 weeks, M213

value: 6% EtOH


title: Jurkat miR-93 -/- #2 total fraction IgG replicate 1

description: total fraction (= input)

source_name: miR-93 knockout cells #2


title: D3_KO_Rep1

description:
d3/bam/mm39/BM_D3_KO1_S3_R1_001.bam
featureCounts.d3.mm39.vM27.txt


title: Dataset 1: NMuMG shPCBP1 FAM3C KO cell line clone #2

description:
5107-MR-59_6_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: Mammary gland

value: NMuMG

value: Epithelial


title: Caput, 6% EtOH, 10 weeks, M212


title: D3_WT_Rep2

description:
d3/bam/mm39/BM_D3_WT2_S2_R1_001.bam
featureCounts.d3.mm39.vM27.txt

source_name: WT cells, d3

value: WT

value: LCMV Armstrong


title: Caput, Control, Cessation, CM21

value: Control-Cessation


title: Caput, 6% EtOH, 10 weeks, M211


title: Jurkat parental total fraction Ago2 replicate 2

description: total fraction (= input)

value: Jurkat


title: Dataset 1: NMuMG shPCBP1 FAM3C KO cell line clone #1

description:
5107-MR-59_5_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt


title: Jurkat parental total fraction IgG replicate 2

description: total fraction (= input)


title: Jurkat miR-93 -/- #2 total fraction Ago2 replicate 1

description: total fraction (= input)


title: Jurkat miR-93 -/- #1 total fraction Ago2 replicate 1

description: total fraction (= input)


title: Dataset 1: NMuMG shPCBP1 CT cell line clone #3

description:
5107-MR-59_4_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: Wild type

value: shRNA knockdown of PCBP1


title: Jurkat miR-93 +/+ control total fraction Ago2 replicate 1

description: total fraction (= input)


title: P14_WT Endothelial  [WT9-EC_S3]

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
STAR (v2.7.9a) was used for alignment of the reads to the reference genome and to generate gene-level read counts.
R package DESeq2 was used for data normalization and differentially expressed gene identification for mutant versus wild type of astrocyte and endothelial cell respectively
Assembly: Mus musculus reference genome version GRCm39
Supplementary files format and content: In excel file format, including Raw read counts data

source_name: P14_WT Endothelial

growth_protocol: All mice were bred in house and housed maximum five per cage with free access to food and water.

extract_protocol:
RNA was extracted from endothelial cells and astrocytes by adding 300 µl of Trizol (ThermoFisher) to the cell pellet, then RNA was purified using the Direct-zol RNA Microprep (R2060, ZYMO RESAERCH), according to manufactures protocol, and eluted in 15 µl of DNase/RNase-free water
RNA-Seq Libraries were generated using the TruSeq strand mRNA kit (Illumina). The RNA-Seq libraries were quantified by Qubit and qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-1000 chip. The RNA-Seq library sequencing was performed using Illumina NextSeq 500.

treatment_protocol: To assess astrocyte coverage/density, Aldh1l1-eGFP (BAC) males (Jackson laboratory, Stock No. 026033; B6 background) were crossed with WT “Noncarrier” females (Jackson laboratory). Conditional knockout of Hmgb1 was achieved by breeding Aldh1L1-Cre/ERT2 BAC transgenic male animals1 (Jackson laboratory, Stock No. 031008; C57BL/6N-congenic background) into a background of female mice carrying a loxP-flanked Hmgb1 gene (Hmgb1flx/flx)2 (Jackson laboratory, Stock No: 031274; B6 background). Animals were backcrossed to generate Hmgb1flx/flx offspring with or without Aldh1L1-Cre/ERT2. Offspring and breeding pairs were all confirmed by PCR. Littermate mice of both sexes were included in experiments at age postnatal day P14.

value: Cortical tissue

value: Cortical endothelial cells

tag: sample group

value: P14 mouse brain endothelial


title: Dataset 1: NMuMG shPCBP1 CT cell line clone #2

description:
5107-MR-59_3_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt


title: Caput, Control, 10 weeks, CM42

value: caput

value: Control


title: Caput, Control, 10 weeks, CM6


title: Caput, 10% EtOH, 10 weeks, EM9

value: 10% EtOH


title: Dataset 1: NMuMG shPCBP1 CT cell line clone #1

description:
5107-MR-59_2_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt


title: Jurkat parental total fraction Ago2 replicate 1

description: total fraction (= input)


title: Jurkat miR-93 +/+ control total fraction IgG replicate 1

description: total fraction (= input)


title: H12-107

city: Ames

first: James

last: Koltes

state: Iowa

address: 1221 Kildee Hall

department: Department of Animal Science

institute: Iowa State University

data_processing:
Adapter and low-quality bases were removed using the bbduk.sh program in BBtools software
Reads less than 20 bases and quality score (Phred + 33) ≥ 20 were filtered out
Reads were aligned against  the reference genome (Suscrofa11.1) using STAR and the RNA quantification (Counts) using FeatureCounts
Assembly: Pig/Suscrofa11.1
Supplementary files format and content: tab-delimited text files raw counts values for each Sample

organism: Sus scrofa

source_name: Muscle

extract_protocol:
Total RNA was isolated and purified from jejunum mucosa, kidney cortex, and liver tissues using the Qiagen RNeasy Plus Mini Kit (Germantown, MD, USA) per the manufacturer’s instructions. For the longissimus dorsi muscle samples, the Qiagen RNeasy Fibrous Tissues Mini Kit (Germantown, MD, USA) was utilized for total RNA isolation and purification per the manufacturer’s instructions.
RNA libraries were constructed using 3’ mRNA-seq QuantSeq technology (Lexicogen, 194 Greenland, NH).

treatment_protocol: Two dietary treatments were evaluated using different concentrations of xylose: a semi-purified xylose-free diet (CTL) and the same diet with 8% D-xylose (DuPont Nutrition & Health, Copenhagen, Denmark)

value: Muscle

value: Xylose treatment

tag: diet supplementation

value: 8percent D-xylose


title: P14_WT Endothelial  [WT5-EC_S1]


title: H11-100


title: P14_WT Endothelial  [WT22-EC_S7]


title: Caput, Control, 10 weeks, CM5


title: Dataset 1: NMuMG shPCBP1 LIFR KO cell line clone #3

description:
5107-MR-59_10_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: Mammary gland

value: NMuMG

value: LIFR -/-

value: shRNA knockdown of PCBP1, CRISPR KO of LIFR


title: Jurkat miR-93 -/- #1 total fraction IgG replicate 1

description: total fraction (= input)

source_name: miR-93 knockout cells #1


title: Dataset 1: NMuMG shPCBP1 FAM3C/LIFR Double KO

description:
5107-MR-59_11_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: Epithelial

value: FAM3C -/-, LIFR -/-

value: shRNA knockdown of PCBP1, CRISPR KO of LIFR, CRISPR KO of FAM3C


title: H09-96


title: P14_Mut Endothelial  [MUT2-EC_S9]

source_name: P14_Mut Endothelial

value: P14 mutant mouse brain endothelial


title: D3_WT_Rep1

description:
d3/bam/mm39/BM_D3_WT1_S1_R1_001.bam
featureCounts.d3.mm39.vM27.txt

value: WT

value: Day 3

value: LCMV Armstrong


title: P14_Mut Endothelial  [MUT21-EC_S15]

value: Cortical tissue

value: Cortical endothelial cells


title: Jurkat parental total fraction IgG replicate 1

description: total fraction (= input)

source_name: Parental cells

value: Jurkat


title: H06-97

value: Muscle


title: Dataset 1: NMuMG shPCBP1

description:
5107-MR-59_1_S1
Processed Dataset 1 - NMuMG shPCBP1 vs FAM3C KO vs LIFR KO.txt

value: Wild type

value: shRNA knockdown of PCBP1


title: CV1.eSPR transduced primary human macrophages donor 4

first: Siqi

last: Chen

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

data_processing:
RNA-seq raw data were analyzed using Partek Flow.
Briefly, sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a).
Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization).
Differentiated gene expression analysis (DESeq2) were performed to generate raw counts
Assembly: hg38
Supplementary files format and content: tab delineated text file include raw counts

source_name: CD14+ selected monocytes differentiated macrophages

extract_protocol:
Total mRNA was extracted at 48 hour post transduction using Qiagen RNeasy Kits following the manufacture’s protocol.
1 ug ofRNAwas used for cDNA library construction and bulk RNA sequencing were performed by Novogene (Sacramento CA).

tag: individual

value: donor 4

value: Adenvirus transduced


title: P14_Mut Endothelial  [MUT18-EC_S13]


title: CV1.eSPR transduced primary human macrophages donor 2

value: donor 2

value: CD14+ selected monocytes differentiated macrophages


title: DP-Rag1ko-CBEwt-Ea-bait2-3C-HTGTS

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-wise chromatin interactions for 3C-HTGTS data processing. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained through spliting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exactly alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph file using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph file using CPM (Counts Per Million in cis) normalization method, and visualized on IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6). The analysis of the correlation for experimental repetition used the R package corrplot(v.0.92).
Pair-wise chromatin interactions for 4C data processing. Paired-end reads were obtained through quality filtering and adapters trimming using fastp (v0.20.0). Notablely, 4C reads which contain a secondary restriction enzyme were removed crosslinks after digesting with the primary restriction enzyme MboI and ligating, so more additional fragments from secondary restriction enzyme digestion and ligation should be discarded necessarily. The first digested fragment for the primary restriction enzyme MboI behind the bait was only extracted and mapped to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive) in the form of single-end reads, and we extracted concordantly exactly alignments using SAMtools (v1.9). We again filtered the self-ligation reads and off-targeted reads, etc.. For visualization, we converted the final bam files into bedGraph file using Bedtools (v2.29.2). Reads numbers were counted and normalized by CPM (Counts Per Million in cis) normalization method per sample, and then visualized on IGV genome browser. The analysis of the correlation for experimental repetition used the R package corrplot (v.0.92).
Three-way chromatin interactions for 3C-HTGTS data processing. As the 3C-HTGTS analysis of pair-wise chromatin interactions, Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing Nested primer or Adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then multiple digested fragments for the restriction enzyme MboI behind the bait were splited and individually aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive) in the form of single-end reads, and we extracted concordantly exactly alignments using SAMtools (v1.9). We converted the final bam files into bed file using Bedtools (v2.29.2). The self-ligation fragments and off-targeted fragments were filtered after mapping. Subsequently, we put all the digested fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. In order to create contact matrices, we directly extracted the first two digested fragments except for the fragment where bait was located, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3-kb, 5-kb, 10-kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Visualization of three-way contact matrices was done with the R package GENOVA (v1.0.0) then differential analysis and visualization of local interactions from three-way interactions were obtained using the Bioconductor package DESeq2 (v1.34.0, p < 0.001). Loops seen on IGV genome browser were called using fixed-size bin resolutions from 3-kb to 10-kb. Briefly, interaction loops (contact frequencies >= 20) were identified through using raw contact frequencies. The distribution for the frequencies of unique reads containing the pair-wise and multi-way chromatin interactions was counted after aligning and filtering, and visualized with the Bioconductor package ggplot2 (v3.3.6).
Three-way chromatin interactions for 4C data processing. As the 4C analysis of pair-wise chromatin interactions, adapters of the paired-end reads were trimmed with fastp (v0.20.0). We only retained reads that were separated by sites associated with the first restriction enzyme MboI. In other words, only fragments with two or more primary restriction enzyme sites were considered for identification of multi-way interactions. Multiple digested fragments for the primary restriction enzyme MboI behind the bait were splited and individually aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive) in the form of single-end reads, and we extracted concordantly exactly alignments using SAMtools (v1.9). We converted the final bam files into bed file using Bedtools (v2.29.2). We filtered the self-ligation fragments and off-targeted fragments after mapping. Subsequently, we put all the digested fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. In order to create contact matrices, we directly extracted the first two digested fragments except for the fragment where bait was located, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3-kb, 5-kb, 10-kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Also similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Heatmap of three-way contact matrices was done with the R package GENOVA (v1.0.0) and the distribution for the frequencies of unique reads containing the pair-wise and multi-way chromatin interactions was counted after aligning and filtering, and visualized with the Bioconductor package ggplot2 (v3.3.6).
Assembly: mm10
Supplementary files format and content: bedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample. we used the custom script to get bedpe files for interaction loops identified by using raw contact frequencies.  The custom utility was used to convert the raw contact frequencies into sparse .matrix format, and  these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions.
Library strategy: 3C-HTGTS

source_name: Thymocytes

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol: For 3C-HTGTS, mouse thymus and liver were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer. And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp or 250 bp paired-end reads.

value: Thymus

value: DP thymocytes


title: CV1.eSPR transduced primary human macrophages donor 3

value: donor 3


title: CV1.eSPR transduced primary human macrophages donor 1

value: donor 1


title: D11-114

value: Xylose treatment

value: 8percent D-xylose


title: H01-98


title: P14_Mut Endothelial  [MUT13-EC_S11]

value: P14 mutant mouse brain endothelial


title: P14_WT Endothelial  [WT19-EC_S5]

value: Cortical tissue

value: P14 mouse brain endothelial


title: untreated primary human macrophages donor 5

value: donor 5

value: untransduced


title: D10-117

value: Muscle


title: A4.eSPR transduced BMDM replication 3

data_processing:
RNA-seq raw data were analyzed using Partek Flow.
Briefly, sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a).
Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization).
Differentiated gene expression analysis (DESeq2) were performed to generate raw counts
Assembly: mm10
Supplementary files format and content: tab delineated text file include raw counts

value: bone marrow derived macrophages


title: A4.eSPR transduced BMDM replication 2


title: A4.eSPR transduced BMDM replication 1


title: P14_WT Astrocytes  [WT5-AST_S2]

source_name: P14_WT Astrocytes

extract_protocol:
RNA was extracted from astrocytes by adding 300 µl of Trizol (ThermoFisher) to the cell pellet, then RNA was purified using the Direct-zol RNA Microprep (R2060, ZYMO RESAERCH), according to manufactures protocol, and eluted in 15 µl of DNase/RNase-free water
RNA-Seq Libraries were generated using the TruSeq strand mRNA kit (Illumina). The RNA-Seq libraries were quantified by Qubit and qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-1000 chip. The RNA-Seq library sequencing was performed using Illumina NextSeq 500.

value: Cortical astrocyte

value: P14 mouse brain astrocyte


title: CV1.eSPR transduced primary human macrophages donor 5

value: Adenvirus transduced


title: D07-112


title: P14_WT Astrocytes  [WT22-AST_S8]


title: untreated primary human macrophages donor 4

value: donor 4

value: CD14+ selected monocytes differentiated macrophages


title: untreated BMDM replication 3


title: untreated primary human macrophages donor 3


title: H03-95


title: untreated BMDM replication 2


title: P14_WT Astrocytes  [WT19-AST_S6]


title: untreated BMDM replication 1


title: untreated primary human macrophages donor 2

value: donor 2


title: P14_Mut Astrocytes  [MUT2-AST_S10]

source_name: P14_Mut Astrocytes

value: P14 mutant mouse brain astrocyte


title: D03-118


title: untreated primary human macrophages donor 1

value: donor 1


title: D05-113

value: Xylose treatment


title: D02-111

value: 8percent D-xylose


title: P14_WT Astrocytes  [WT9-AST_S4]


title: P14_Mut Astrocytes  [MUT21-AST_S16]


title: C3_input

city: Zhengzhou

first: Shuaiyin

address: No. 100 Kexue Avenue, Zhengzhou

institute: Zhengzhou University

description:
Ctrl_IPVSCtrl_input_peak.txt
genes_fpkm_expression.txt
isoforms_fpkm_expression.txt

data_processing:
library strategy: MeRIP-Seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
HISAT2 (http://daehwankimlab.github.io/hisat2) was used to map reads to the reference genomeHomo sapiens(Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCH38
Supplementary files format and content: tab-delimited file include gene fpkm values for each sample
Supplementary files format and content: tab-delimited file include transcript fpkm values for each sample

molecule: polyA RNA

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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 withE. coliDNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp.

tag: cell line

value: RD cell


title: P14_Mut Astrocytes  [MUT18-AST_S14]

value: Cortical tissue

tag: cell type


title: H10-102

tag: treatment

value: Control

value: Xylose-free (0percent)


title: C2_input


title: NP137-treated LKPR sample 1 (Visium)

city: Brussels

first: Sebastiaan

last: Vanuytven

address: Campus Erasme CP 637

country: Belgium

institute: Université Libre de Bruxelles

description: FFPE spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Rangers default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5
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: hires 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: skin

extract_protocol:
Control and NP137-treated skin tumours from LKPR mice were dissected, rinsed one part of the tumors has been kept for immunochemistry. Tumour tissues were pre-fixed in 4% PFA for 2 h at room temperature, rinsed in PBS, before to be embedded in FFPE
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's recommendations

value: skin

value: NP137 In vivo IP


title: Control LKPR sample 1 (Visium)

description: FFPE spatial transcriptome sequencing

value: Control N/A


title: H08-99

value: Muscle


title: NP137-treated LKPR sample 2

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Quality control and downstream analysis were performed using the Seurat R package (v.3.1.5). For each sample, all of the cells passed the following criteria: showed expression of more than 600 and less than 8000 unique genes and had less than 25% UMI counts belonging to mitochondrial sequences.
Read counts were normalized by NormalizeData function of Seurat, with parameter ‘normalization.method = LogNormalize and scale.factor=10000’.
A PCA for each sample was calculated using the scaled expression data of the most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes).
UMAP calculation and graph-based clustering were done for each sample using the appropriate functions from Seurat (default parameters) with the respective PCA results as input.
In addition, to verify proliferating stages, the  S-phase and GS/M-phase scores were regressed out by CellCycleScoring function, implemented in the Seurat.
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Control and NP137-treated skin tumors from LKPR mice were dissected, rinsed and digested in collagenase type I (Sigma) at 3,5mg/ml in HBSS (Gibco) for 1h at 37°C on a rocking plate protected from the light. Collagenase was blocked by the addition of EDTA (5mM) and then the cells were rinsed 1 time in PBS supplemented with 10% FBS and the cell suspension were filtered through a 70-μm cell trainer (BD Bioscience). For the wash next and antibody incubation, cells were resuspended in PBS supplemented with 2% FBS (facs buffer). Cells were incubated with BV711- conjugated anti-EPCAM (rat, clone G8.8, BD Bioscience Cat#563134, dilution 1:100), PE-conjugated anti-CD45 (rat, clone 30-F11, BD, Cat#553081, dilution 1:100) and PE-conjugated anti-CD31 (rat, clone MEC 13.3, BD, Cat#553373, dilution 1:100) antibodies for 30 min at 4 °C protected from light. For cell sorting, cells were also filtered through a 40-μm cell trainer (BD Bioscience). Living single tumor cells were selected by forward and side scatter, doublet discrimination and Hoestch exclusion. Profile of the tumors was analyzed following viability and profile of YFP, Lin- (CD45/CD31) and EPCAM expression. Once screened all lived cells were sorted for single cell RNA sequencing experiment using FACSAria and FACSDiva software (BD Bioscience)
10,000 single cells from the LKPR tumor were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).

treatment_protocol: To determine the effect of anti-Netrin-1 molecule (NP137) on primary tumor, LKPR mice were treated intraperitoneally at 10 mg/kg every two days from 4 weeks after Tamoxifen injection and until the death of animal.


title: H07-105


title: C1_input


title: C3_IP


title: P14_Mut Astrocytes  [MUT13-AST_S12]

value: Cortical astrocyte


title: NP137-treated LKPR sample 1

description: 10x Genomics


title: Adult heart, 8W,  replicate2, RNA-seq

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver 10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10).
CLC Main Workbench(Ver 21.0.4, Qiagen) was used for the downstream analysis.
Supplementary files format and content: Microsoft Excel file  with raw counts, normalized expression values and transformed values for every gene

source_name: Whole ventricle

extract_protocol:
For MEF, RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). For whole heart, mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. After the heart was harvested, the atria and valves were removed, and  RNA was extracted using Trizol reagent.
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)

value: Whole ventricle

value: 8 weeks

value: ICR


title: Adult heart, 8W,  replicate3, RNA-seq


title: C2_IP


title: Control LKPR sample 2

description: 10x Genomics


title: H02-94


title: Embryo heart, E12.5,  replicate3, RNA-seq

value: Embryonic day 12.5


title: C1_IP


title: Embryo heart, E12.5,  replicate2, RNA-seq


title: H04-106


title: D09-116


title: Control LKPR sample 1

description: 10x Genomics


title: Adult heart, 8W,  replicate1, RNA-seq


title: D12-109


title: EP+ KD Ntn1 2

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Assembly: Mm10 / Grcm38.87
Supplementary files format and content: .csv / normalized gene expression with annotation

extract_protocol:
RNA extraction from FACS-isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations.
Indexed complementary DNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: LKPR EPCAM+

value: Epithelial cells

value: Netrin-1 Knock-down


title: EP+ KD Ntn1 1


title: Donor 6323, Relapse 2

city: Galway

first: Eva

last: Szegezdi

address: University Road

country: Ireland

institute: University of Galway

description:
10X Genomics
6323_R2

data_processing:
Reads were aligned and quantified using CellRanger v6.0.0. Cell type annotations were predicted using the dataset from Granja et. al. (GSE139369) as a reference.
Assembly: hg38
Supplementary files format and content: Processed data is provided as tab-delimited text files. For each sample there are two files: a cell (rows) x gene (columns) count matrix and a metadata file with cell type annotations for each cell.

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow aspirates were obtained from The Finnish Haematology Registry and Clinical Biobank. The mononuclear cell fraction was isolated using Ficoll density gradient separation.
Cell counting and viability assessments were conducted using To-Pro-3 viability dye. Thereafter, GEM generation & barcoding, reverse transcription, cDNA amplification and 3’ gene expression library generation steps were all performed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Single Index) User Guide (10x Genomics CG000204 Rev D) with all stipulated 10x Genomics reagents.

value: Bone marrow aspirate

tag: subject id

value: Donor 6323

tag: time point

value: Relapse 2


title: Donor 6323, Relapse

description:
10X Genomics
6323_R

tag: tissue

value: Relapse


title: Donor 6323, Minimal residual disease

description:
10X Genomics
6323_MRD

value: Minimal residual disease


title: D08-115

value: Control

value: Xylose-free (0percent)


title: Embryo heart, E12.5,  replicate1, RNA-seq


title: iCM, GT_M2TAD,  replicate3, RNA-seq

source_name: mouse embryonic fibroblast

value: mouse embryonic fibroblast

value: 4 weeks after transduction

value: GTM2TAD transduced MEFs


title: D06-108

value: Muscle


title: EP+ Empty vector 2

value: skin

value: control


title: Donor 6323, Diagnosis

description:
10X Genomics
6323_Dg

value: Diagnosis


title: H05-104


title: EP+ KD Unc5b 1

value: LKPR EPCAM+

value: Unc5b Knock-down


title: iCM, GT_M2TAD,  replicate2, RNA-seq

value: ICR


title: EP+ KD Unc5b 2

value: Epithelial cells


title: Donor 5750, Relapse

description:
10X Genomics
5750_R

value: Bone marrow aspirate

value: Donor 5750


title: iCM, GT_M2TAD,  replicate1, RNA-seq


title: Donor 5750, Minimal residual disease

description:
10X Genomics
5750_MRD


title: D01-110


title: EP+ Empty vector 1


title: iCM, GT_M2,  replicate3, RNA-seq

value: GTM2 transduced MEFs


title: Donor 5750, Diagnosis

description:
10X Genomics
5750_Dg


title: iCM, GT_M2,  replicate2, RNA-seq


title: G12-64

source_name: Liver

value: Liver

value: Xylose treatment

value: 8percent D-xylose


title: iCM, GT_M2,  replicate1, RNA-seq

value: mouse embryonic fibroblast


title: Donor 5143, Diagnosis

description:
10X Genomics
5143_Dg

value: Donor 5143


title: G11-60


title: MEF, Ctrl, replicate3, RNA-seq

value: 4 weeks after transduction

value: MEF


title: HeLa cells, TBLR1-overexpressed 2

first: Yifang

last: Mao

state: Other (Non U.S.)

address: 58 Zhongshan Second Road, Guangzhou

institute: Sun Yat-sen University

data_processing:
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation
Assembly: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default
Supplementary files format and content: tab-delimited text file include raw counts of each sample
Supplementary files format and content: tab-delimited text file include RPKM of each sample

source_name: HeLa cell

growth_protocol: Cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), which consisted of 10% fetal bovine serum and 1% antibiotics and then stored in a 5% CO2-humidified atmosphere at 37.0℃.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: HeLa cell

value: cervical cancer cell


title: HeLa cells, TBLR1-overexpressed 3


title: HeLa cells, TBLR1-overexpressed 1


title: HeLa cells, control 3

value: WT


title: G09-68


title: Donor 5143, Relapse

description:
10X Genomics
5143_R

value: Relapse


title: Donor 4978, Minimal residual disease

description:
10X Genomics
4978_MRD

value: Donor 4978

value: Minimal residual disease


title: MEF, Ctrl, replicate2, RNA-seq

value: ICR


title: HeLa cells, control 1


title: G03-57


title: D04-119

value: Muscle

value: Control

value: Xylose-free (0percent)


title: HeLa cells, control 2


title: G01-62

value: Liver